I can vouch, from my own 600 adventures, that ClassicWB 68k is the best option for a vanilla 600. GAAE is nice and comes with lots of extras. Standard 68k version is great but basic comapred to GAAE. but it's got everything you would need to get you up and running with the minimum of fuss.
This about replacing that KickStart so you can use the other versions. Also think of getting an accelerator, or at the very least look at a way of expanding RAM, if your wanting to play with WHDLoad.
A great tool is Amiga 911 boot disk. This comes with some tools for configuring a HDD. And I would say do everything in WinUAE first and then transfer over.
Oh and make sure the max transfer is set right to 0x1FE00 for the partitions. Otherwise it will cause isssues in a real Amiga.
