i ran with the set up in picture number 3, as it made the most sense. it works great.
just a foot note: i also bought the self bleeders from (help), man i had never used these things and i want to tell you they are great. i had the system bleed in less that 10mins. those things are awesome. i just used a piece of rubber hose over the bleeder valve and ran it into a coke can. no mess!!!!