There is a way to make territories have perfect borders when they first don't. But it's a more slow way than it would be had you made the territories perfect from the start.
Here's an example:
Let's assume I'm making an earth map, and I have two territories drawn:
As you can see the borders don't overlap that well, but I think the right territory is closer to reality than the left one. Now, to make the left one overlap perfectly with the right, I first create a duplicate of the right territory by by selecting it and pressing CTRL+D. Then I double-click the territory I think has a faulty border, to go in the nodes mode, like this:
And I drag the corresponding nodes across the border with the right territory, until there's no more gap, like this:
Then I select both territories (not by dragging a box around them, this makes the method fail. You click one of them, then hold SHIFT and click the other one), and use this tool, under the paths menu:
Once again, I have no idea how it's called in English, but you can recognize the symbol.
Now the result should look something like this:
Don't be afraid, you didn't screw anything up, the copy of the right territory is still there beneath the thing you've just created! Now, go in the nodes mode again by double-clicking it, and select a few nodes that belong to the right territory, and press DELETE. You don't need to select all of them, a few will do. Now, this action will leave you with a long, curved line, not anywhere near any territory borders. Just click it, press DELETE, repeat until it's gone. And the result is this:
Sometimes, the last step may cause you to delete nodes belonging to the wrong territory. But, as you grow some experience with Inkscape, you should be able to fix it quite easily.