You might want to stick with OBMM until you're more comfortable with Wrye in general. I've been running Oblivion for years and I still use OBMM and don't use BAIN. I know a lot of people swear by it, but I found it just too hard to use. Now in my case it was partly because I was only using it to install mods that came as BAIN packages... Anyway I'm quite comfortable with OBMM and have gotten pretty good at detecting conflicts. Wrye and I are finally starting to get along after years of battles
Ironically, one of the things that BAIN doesn't do so well are texture replacers. I suggest sticking with OBMM and getting used to the tools it has. DO NOT use it for conflict detection. When you install something and it asks about displaying conflicts, answer Yes and have a look at the files that conflict and make a decision on which mod you want to override another. Installation order is very important. BAIN is apparently better at listing files in conflict, but having not used it myself, I don't know what form that takes. Don't run the conflict detector utility in OBMM - basically it doesn't work. I suggest you get used to using the Info option when you right-click on an omod - this tells you the files that make up a mod. You can use this to identify potential conflicts.
Don't worry about what QTP3 talks about in terms of archive invalidation and what-not. The information is outdated. Wrye will install a file called ArchiveInvalidationInvalidated!.bsa for you when you install it. Your Oblivion.ini file should have a line in it like this:
SArchiveList=Oblivion - Meshes.bsa, ArchiveInvalidationInvalidated!.bsa, Oblivion - Textures - Compressed.bsa, Oblivion - Sounds.bsa, Oblivion - Voices1.bsa, Oblivion - Voices2.bsa, Oblivion - Misc.bsa
That's it! Archive Invalidation has been taken care of. OBMM also has a mechanism for doing archive invalidation that Tomlong prefers. If you are ready her guides, then that is the method she will tell you to use. You can do that instead if you like. That's part of the problem in trying to read all this material - everybody has their own opinion on how things should be done and you need to go through it all and choose the best one for you!
Lastly, if you are installing a mod that has been packaged for BAIN, it will need a directory called 'omod conversion data' for you to install it with OBMM. It it doesn't have that, then you will have to unzip the files to another location and repackage it for OBMM. This is what I do now. I have a directory called GameRepository where I put all the mods that need work of some sort and fix them up there. Then I create archives and create an omod from those archives. Just a suggestion - once again you will need to decide what works best for you.