I used to unplug then plug it back in when I started off that way it was easier to boot leaving the dongle in and it was fine. You dont have to leave it unplugged at all just take it out and put it back in and it is ready for jailbreak next boot. I now have the hub that turns the 2 usb ports into 4 and looks like it as meant to be there. Any how with a hub plugged in you can have the hdd and dongle in always and never any need to remove. The dongle and usb hdd have to be plugged into the same shared port for this to work but removes alot of hassle jailbreaking. Pair that with a g-switch so there is never a need to unplug the ps3 again and wear out your socket as mine got loose quickly but a hub and switch makes everything much less archaic.
PS3 CECH-2501A [CFW] & CECH-3001 [OFW]/ PS2 SCPH-3901 & SCPH-7501/ PS1 SCPH-5501
Mod Cobra 4.46 v7.00 w/ E3 Flasher [CFW] & Cobra ODE 4.50 [OFW]/ Mod HDD-OSD [Phat] & Modbo 4.0 [Slim]/ Mod MM3
HDD 1tb [CFW] & 640gb [OFW]/ HDD 640gb & OPL v0.92 w/ 1.5tb SMB