Its probably easier to install ToB now rather than later. If nothing else, youll save on having to download both fixpacks.
Anyway. Install the official patch and then the fixpack. You now have what is generaly considered the standard version of BG2. What I do is copy dialogue.tlk, chitin.key and my override folder somewhere, so that if a mod does screw one of them up I can simply replace them and be back at a stable version.
I would skip the XPcap remover, they tend to screw things up. But a "safe" one is OK I guess. ToB is better though. Install it after the fixpack, along with the rest of the baldurdash tweaks.
Now, some of the SoA tweaks dont work with ToB installed, and kevin hasnt marked which do and which dont. To my knowledge, the bonus merchants and the "shut up" packs work.
I suspect that extended spell tables will screw up since ToB has new spells. Might work, might not. Universal Ioun stones will probably work, but only for the stones in SoA. ToB only stones wont be affected. There may be ToB versions of the tweaks, if so use them instead.
The key point when installing these mods is that the files end up in the override directory. Most zips are set up so that extracting to the BG2 folder will put them in override automaticaly. Certainly all baldurdash ones should work like that, other sources might not. Safest is to extract to a temp folder and copy by hand.
Some mods are more complex. Used to be that installing more than one of those mods was suicide, the files would conflict and youd end up in a mess. Nowadays we have weiDU. To install a weiDU mod, extract it to your BG2 folder, go into the mod folder it just created, and run its install program. Follow the instructions, and let the program take care of the details.
To save your save-files, simply copy the save folder in your BG2 folder somewhere safe.
Finaly, for a rookie its probably best to stick close to the standard game. Improved mods are tougher, which is fun if you know what your doing but first time through will probably be frustrating.
www.teambg.com is a good place to find them though.