I don't keep any unused/inactive ESP or ESM files in my data folder. Instead, I place them in a sub folder within the Data one and take them out when wanting to use them.
Actually, that's quite a good idea. Well thought-out.
A slightly better idea: Wrye Bash actually includes this as a function. If you right-click on any mod, one of your options is "hide." This moves the file to another folder, outside of the Data folder. The advantage of moving the files outside Data is that the entire Data folder loads when you load up Oblivion - all files, active or not. And, there is a hard limit as to how many esp + esm files (total, active or not) that you can have in your Data folder before the game starts crashing. The limit is 255 or so, I think. I'm not positive; the info is around the boards somewhere. And, if you keep modding, chances are that one day you'll approach the limit and start worrying about it. So, using Wrye Bash's "hide" function now is just good practice.
As for merging, to be honest, I have no idea how to do that. I was thinking perhaps near the end I would attempt it unless of course its prudent to do it now?
You should build the bashed patch (which includes merging) before you run the game at any point. And it would be a good idea to run the game at the end of your basic FCOM install, before loading anything else, to test things out, make sure everything's okay.
Building the bashed patch is easy. Essentially, you right-click on the bashed patch, which automatically appears in your load order, and choose "Rebuild Patch." Then a window pops up and you choose from among many options (this part you can get help on when you get there), and then it builds itself.
So the BOSS log should only be showing ones I have activated - right?
Yes. However, inevitably something will go wrong (sort of like plumbing), and, when it does and you ask someone for help (the plumber), they will ask at some point to see the load order (the leak) for themselves. It has nothing to do with trusting or not trusting you or BOSS. It's just that, when troubleshooting, your helper wants the evidence to be as close to first-hand as possible. Thus, posting the load order from Wrye Bash is just, in general, a better approach.
gothemasticator