I bought the GOG versions of both BG1 and BG2, so having finished BG1, I am now starting BG2. At launch, there are two choices; however, I am a little confused as to which one I should start with, "Shadows of Amn" or "Throne of Bhaal".

My main objective here is to do ALL the quests and explore ALL parts of the original game and the expansion. My understanding is that ToB is the expansion pack, so is there a reason I would select that? Does it just assume you've already done most/all of SoA?

Does SoA have the original content PLUS the expansion pack, making it the ideal route? I have read the descriptions the game provides at start-up, but I was still a tad flummoxed.

Or, would I select SoA, and then hit ToB?

Sorry for the noob questions, but I'm pretty much a noob in the Realms.

Short answer: start SoA

Long answer:

When you have finished BG1,
copy the final save of BG1 to the save folder of BG2 or export your main char in BG1 and copy the file
to the caracter folder in BG2.

SoA means "Shadows of Amn"
It is the original BG2 and it starts after the end of BG1.
There you can already enter the watching fortress (exact name forgotten, a ToB bonus dungeon)
Once you beat the final Boss of SoA, the game automatically continues with ToB.

ToB means "Throne of Bhaal"
It is the expansion of BG2 and it starts where the original BG2 (thats SoA) ends.
You start with a high level char and some items from SoA.

The best thing is to create a level 1 char at the beginning of Bg1 and use this char for BG1 and BG2 (SoA and ToB)
I think BG1 is harder than BG2 (except some optional fights maybe).
When your char finished BG1, he will be good enough for Bg2 too.

The option to start ToB is there ONLY if you want to play it standalone with a brand new (or imported) character. If you go through SoA, at the end the transition to ToB is automatic with your current SoA character and team. So choose SoA unless you ONLY want to play ToB.

The BG2 expansion pack isn't quite like the BG1 one. In BG1 it adds (relatively) high level content to the main game in the form of Durlag's Tower, etc, which you can theoretically do at any time (though as you'll know having finished it, it's advisable to wait until near the end of the game so you have enough power). The BG2 expansion, ToB, is more focussed on the story, and continues the plot of the game beyond the end of vanilla BG2 (that is, SoA). When you finish playing the vanilla game, it'll automatically move you on to the expansion's content and plot. There's also one mega-dungeon, with multiple levels in the style of Durlag's Tower. It's called Watcher's Keep, and can be accessed from either vanilla BG2 or ToB. Since the maps for SoA and ToB are of slightly different areas, this is the only location which can be accessed in both, so be careful about storing items before the final SoA battle and expecting to get them back later!

The ToB button is if you wanted to start with the ToB content (that is if you'd bought the expansion later on, and had already played SoA and wanted to skip past it). You want to click on the SoA button. Incidentally, if at some point you play with BGT (Baldur's Gate Trilogy, a mod which combines BG1 and 2 into one game running in the BG2 engine), you'll also want to select SoA to start.