There have been loads of similar threads, have a search around, people aren't inclined to answer the same questions again
From my perspective :
There are loads of differences DBPro is a completyely re-written engine. YES you can use Pro without having to own or know DB1
The best reasons to use pro are: IMHO
Much faster
More stable in XP
Split screen possible
Many new Shadowing and lighting effects
Proper file accessing and editing
DLL support & Online Multiplayer (You CAN do this in DB1 but need to buy Dark Matter expansion)
BSP Support (eventually

)
Basically much more proffessional results are possible
The reasons NOT to use it and stick with DB1 would be ummm
1. Its cheaper and
2. There are less bugs (but DBP is getting patches all the time to fix this )
To answer your more specific question, the bundle with DB1, um well personally I don't think you need Dark Matter for use with DBPro, cos the models are not that versatile, I would recommend buying a copy of Milkshape3d, it only costs $20 and a demo is downloadable for free
I like the Cartography Shop, but many people recommend Quark or various other level editors, which are all FREE so you could save yourself some cash.
Infinity textures is quite cool, but in my opinion overpriced. VanB made a really cool similar application for creating seamless textures which is FREE

Also I would recommend a copy of Panit Shop Pro (Shareware, around £70, or £5 for an older version

)
I haven't looked at the bundles but they used to include the3dGameMaker in some of them. PLEASE Don't touch this with a BARGEPOLE. Its awful. No - really. lol
Personally I'd buy DarkBasicPro - just remmember to download and install the latest Patch before you use it - otherwise you'll get a nasty shock

Also don't bother downloading and trying the demo - its a very early bugged version - the one you'll get when you buy it is far, far superior

The only thing you really need to pay for on top of that IMHO is Milkshape
Hope this helps