I've screwed around a little with this kind of thing but have not yet made a 'real' recording. Still waiting on a Granados duet book I ordered weeks ago. It must have circled the globe several times by now and I do wish it would hurry up and get to me!
(sorry - a little rant there.)
Marcelo, I do think that you just need to be able to have both parts down solid. Then just start doing some trial run-throughs. The hand that plays first should be the hand to record first. And when you have a good clean version, listen to it in earphones while you record the other part on top of it.