So, Blackra1n works perfectly fine on my 3Gs right now, but
after a bit more research and finding out whats the problem...
turns out Blackra1n have this glitch that whenever you shut down your iPhone, you will need to connect it back to the comp.
I find this very inconvenient, is there anyway to fix this?
Or how to unlock my iPhone with Pwnage tool, whatever, or something?
It's not a glitch, search for 'tethered jailbreak'.
Maybe your version of Blackra1n jailbreaks new bootrom tethered only. Check you've got the latest version of blackra1n as I'm not sure it has untethered jailbreak now?
Spirit can do untethered jailbreak, but I think you will need to restore first - got SHSH's?