I'll try to sum this up a bit for you; (Some of this has already been stated)
Bulkheads:
They are strictly holes in the tank that will allow water to flow. So, where ever the hole, that is your water level. You can use PVC inside of the tank to add extensions that will regulate the water level.
Once you have the water level in the tank where you like it, then move on to the sump.
Water height in sump filter:
Most people will fill the tank with external hose which will eventually lead to water flowing to the sump. Once you have the pump inlets covered, you have now hit your minimum level. You should then add a few inches water to allow for evaporation and such.
Pumps: Most people use submersible pumps in their sumps, but external pumps plumbed outside of the sump are an option. As stated before, look to the sticky for pump sizing.
Sump Access:
If the sump is designed properly, the only need to access will be to change filter media. This is made easier by having the mechanical filtration closer to the top of the sump for easy reach in access.
Always try to figure in how much room you would need to access any particulars such as heaters. I like to have about 8" of space so that I can fit my big head over the top of the sump to see what's going on if needed.
FX5s:
Bulkheads are a great option for plumbing your canisters because it removes a bit of the unwanted clutter, but it is all a matter of personal preference.
Reference:
I'll try and dig up a couple good designs for you. I do know that jcardona did a great sketch that might help you out. You should try searching his threads.
