1. I'm very rusty on building my own computer since i did it 8 years ago. I have 3 old hard drives (Western Digital WD800JD-22JNC0) and i just got a new motherboard. It has four 3gb sata ports and two 6gb sata ports. Will these be compatible? And will it make a difference if i plug two into the 6gb and one in the 3gb or all in the 3gb?
2. When plugging in my system pannel connectors which way should the cables connect. With the words towards the outside/inside/opposite? I see the words next to the ports so should they face them? I can't find anything in the manual about it and don't want to take my best guess.
Again my knowledge is really rusty on these subjects.
More about :sata iii compatibility system pannel connectors
SATA is forward and backward compatible so it shouldn't make any difference which port you plug the drives into.
I'm not quite understanding your question about how to plug the connectors in. What cables are you talking about? SATA connectors and cables are keyed and it shouldn't be possible to plug them in the wrong way around.