Long before South Sudan became a republic, its leaders made a point of being on the good side of Uganda. They had no choice. After all, this was territory that relied on its neighbours for emotional support and for all sorts of things that come with agitation for Independence.

Now that the South Sudanese have the status their leaders spent a lifetime fighting for, they are in position to make choices that their neighbours may not always like.

Uganda will be monitoring closely how events play out in Juba, where the new leaders — confident as never before — will be cutting deals to get the state running.

Will they defer to presidents like Museveni, who has a track record of military adventurism and a tendency to cajole leaders with less experience? In short, will the South Sudanese accept any patronising behaviour by Uganda?

If South Sudan’s painful — but brave and single-minded — record suggests anything, the answer is not in the affirmative. You wonder, then, how the Ugandans will behave in such circumstances. History suggests that certain mistakes are not to be repeated, with the twin case of Rwanda-Congo providing perhaps the best template for how not to proceed. And current affairs suggest that Uganda is not the regional force it once was, with the East African Community, the trade bloc South Sudan wishes to join at some point, running the show and setting the agenda.

However, the simple fact that Uganda’s influence in the region is significantly diminished, does not mean that Uganda has no real and practical expectations of South Sudan. “We are basically babysitters,” said Angelo Izama, who runs Fanaka Kwa Wote, a Kampala-based think tank on regional politics and security. “In future South Sudan may become a rowdy teenager.”

It is a fitting analogy. As such things go, how the relationship evolves depends partly on how the baby is raised. It is important for Uganda to be a responsible adult, to exercise restraint in the pursuit of its strategic interests, some of which will inevitably be rejected as South Sudan grows older.

“We should keep our distance,” said Phillip Kasaija, a Makerere University political scientist who has studied regional security issues. “We should not be seen to be patronising. We should push our interests, but we shouldn’t be seen to be pushing too hard.”

But what, practically speaking, should the Ugandans do? “They need us as much as we need them, but we must respect the sovereignty of South Sudan,” said Mwambutsya Ndebesa, a political historian at Makerere University. “And we have to be careful not to patronise them. They have other possibilities — Kenya, for example. I don’t think Kenya can meddle in the internal affairs of South Sudan.”

Uganda can learn from past experience — and no scenario provides a better framework than the complications that caused the love-hate relationships Kampala has had with Rwanda and Congo.

A major cause of Uganda’s misadventure in the Democratic Republic of Congo was Kampala’s refusal to accept, in the 1990s, a different order in which the Rwandans claimed a fair amount of power. Mobutu Sese Seko had been defeated with the substantial support of Rwanda, and the tyrant’s exit left Rwanda more emboldened as a state.

At the same time, Kinshasa was getting close to Kigali in a way it was not with Kampala, setting off the chain of events that would be the cause of a protracted hostility between Rwanda and Uganda. Once Rwanda’s Paul Kagame had consolidated power at home, he had little use for someone like Museveni, who liked being deferred to. If Rwanda wanted a mentor up to some point, it seemed that Uganda wanted the role of a patron. Kagame, who used to make endless trips to Kampala, ostensibly to brief Museveni on happenings in the Congo, stopped coming.

The end game, of course, was a series of bloody skirmishes between the countries’ armed forces in the Congo.. The clashes were responsible for a diplomatic fallout from which both countries have not yet fully recovered.

This brings us back to South Sudan, with which Uganda is an ally on paper and in reality. Cross-border trade between Uganda and South Sudan has tripled recently, passing the $150 million mark.

But there are problems beneath the surface, problems that may, on some level, have something to do with the political characters still in place. Museveni and John Garang, the de facto leader of the South Sudanese people until his sudden death in 2005, respected each other, but this may not be entirely the case with Museveni and Salva Kiir, South Sudan’s first president.

Some sources suggest that Kampala does not have much regard for Kiir, who was virtually unknown when Garang was alive. Ugandan politicians have business interests of varying respectability and legality in South Sudan, where their activities will come under more and more scrutiny once Juba starts running normally. Uganda still has military interests in South Sudan, which was long a playing ground for the rebel Lord’s Resistance Army.

Then there is the persistent problem of xenophobia, which has plagued foreigners, not just Ugandans, who wish to live or do business in South Sudan. What is clear is that South Sudan will be trying to impress the whole world, not just Uganda.

With its oil resources, the country has many friends, and so Uganda, accustomed to being called special, may soon find itself in the unusual situation of being ignored sometimes. Courted by everyone from the Chinese to the Kenyans, South Sudan is set to be the strongest economy in the region in two decades or so.

For now, however, the world’s newest county must transition quickly from the poetry of Independence to the prose of governing, and it will not be easy.

South Sudan still has border issues with Sudan, from which it seceded, and the spectre of violence — and another refugee crisis in the region — is always looming.

The country’s leaders must unify the disparate tribal constituencies, build infrastructure, and make the whole country governable, conditions that makes them vulnerable and the target of bullies. They need Uganda to be a friendly neighbour, and at this stage it is difficult to see how Kampala could put up a different performance.

In the matter of a healthy diplomatic relationship, the extent to which Uganda pushes to realise its own interests in South Sudan will matter a lot. There was a time when South Sudan — and Garang in particular — would have done anything to gain the favor of Museveni’s Uganda.

In proxy wars that played out well for both parties, Museveni needed the rebels in South Sudan to torment Kony and the South Sudanese needed Museveni to support their military campaign for Independence.

But those days ended the day Kiir took his oath, and now Uganda must sit back and let South Sudan take care of its own destiny.