Umm.. just pick the cores you want it to use, per slot. There's nothing particularly different about EQ2 from any other game, you are just observing that the Quick Setup Wizard does things differently depending on the game you select. I understand you didn't expect THIS to be different, but the wizard does say that it will select different options depending on the game you select

ISBoxer currently only selects cores automatically for WoW and RIFT (you have this backwards, it was specially ADDED for RIFT, not removed for EQ2). Using the wizard and selecting any other game will select no cores by default. With no cores selected, the game's CPU core selection will be allowed. For RIFT, that meant a setting in rift.cfg that defaults to the same core(s) would be used instead of the rest. (WoW also has a CPU affinity setting, as do other games, possibly even EQ2) Most games (as in the game itself, unrelated to ISBoxer) don't select specific cores by default, in which case leaving the cores unselected in ISBoxer is exactly the same as selecting all of them.
Options are usually only filled in by the wizard when there would otherwise be a problem. So far I haven't heard anyone complain that they get terrible EQ2 performance because of the CPU core selection, but this was a big thing for RIFT.
So... if you want to try it out the same as you had it for RIFT, just select all the cores. Maybe it will perform better, and maybe it wont. Only way to find out how it will best perform is to try it out!
Also, is there any updates that I may need to manage my cores properly? I have an AMD Phenom II X4
No.