It isn't clear what you're planning to do. You should probably try to explain each part individually. If we don't know what you're trying to do, we can't really help you.
That said, merging several conflicting mods into a single mod won't necessarily fix those conflicts. Instead it will force you into having to decide which parts of a mod you want to be used, and which ones you don't. In the cases of non-minor conflicts, this usually means breaking significant portions of the mod. Essentially, if it doesn't work when the individual mods are loaded in game, it won't work any better when you try to merge them. There are exceptions to this (hair, races, eyes), and some things can be negotiated around by spending ALOT of effort rebuilding those aspects (from scratch usually) so that they can work better together. Without knowing what mods you were trying to make work together, and the nature of their current conflicts, not much else can be said. You WILL however need permission from the original authors of those mods if you planned to share the mod with anyone (online or off). Since you are working on this with a friend, I would hope that you have already done that.
As far as learning scripting goes, you might want to try the CS wiki.
http://cs.elderscrolls.com/constwiki/index.php/Main_PageIt should however be noted that learning to script by trying to make conflicting mods work together is probably a very bad idea, and will lead to very much frustration. Few modders leave notes in their scripts, so any changes may break more than you'd think. Instead you should learn scripting by starting out with simple quest mods, then work on spell effects and eventually more complex quests.