Jonboy,
Separate lines definitely. Specially if you are using Jet Tronic valves, the break valve bleeds a lot of air on the off cycle and you loose alot of pressure if you use your breaks while taxiing. Also, I like using a 4 way junction, and route, tank /Gauge/Filler valve and supply line all in one junction. Also you may want to use an orifice on the up or down line for the main retracts to slow it down abit. I would also use quick disconnects with check valve on fuselage side at the junction to the wings. (so that you can check the system for leaks without the wings being plugged in) only for the gears not break line. and try to keep the lines going to each mains same length as much as you can to limit delay between gears.

good luck
jason