I had two level 1 Lucian's, one with belt and one with armor (they both came off the carousel). I had plans to combine the armor into one item, and the belt into a totally different item. However, when I bought my third Luc, noy only did the champs combine, but the two items combined into the corresponding item (red buff).
I don't think this should be the way it goes. I think there should be two basic items on the resulting champ (armor and belt in this case), both uncombined. This leaves open more options for planning for future items, rather than being restrained. The only way I see to go around this currently it to not upgrade until you get the items you want, then combine the items before you upgrade the champ. That's icky.
I'm loving the game all around, but this annoyed me a little bit, because it actually did end up costing me the game (very tangibly and obviously so).