SaVas,
here's the basic concept.
Cut the first half.. paste it on a new canvas or file.
Cut the second half.. paste it on the same canvas as the first half..
Then Align them together

When you have finish painting.. paste it back (You don't have to split them.. just paste and align and then remove the excess areas)
to get a nice alignment.. set ur fuse layer to "multiply"

Here's my opinion on FSRepaint.
I haven't tried out its painting side.. but I think I rather preview my aircraft in FS. The big difference is the lighting.. FS allows you to see how would the plane look like in the afternoon , dusk , dawn , morning..etc so you can tweak the colours accordingly.
So I would recommend a graphics editing software such as paint shop pro or photoshop or g.im.p (free)