Sid there's lots of factors that would affect the type of seperator/charger you would use, so I'll make an assumption you have a good idea what type suits you.
IF the seperator had the ability to allow the second battery to start the car in a pinch (ie the override as discussed in Flashman's case) then you'd want at least 2B&S cable to flow that kind of current.
If it was just a DC/DC charger (such as Redarc BCDC or CTek) then 6B&S would be fine. I think the manufacturers even specify 8B&S (smaller than 6). These type claim to charge the second battery more efficiently, which is great, but don't offer the ability to join the batteries in a pinch, ie for starting from second battery, or to allow it to assist in winching, which is the compromise. Of course you can wire a solenoid seperately just for these situations, depending on how keen you are, that gives you the best of both worlds.
If battery is in the rear, with dcdc type charger that should be as close as possible to second battery, with normal parallel seperator it doesn't really matter, probably more convenient in engine bay. I'd run a fuse block off second battery in a convenient spot down the back, close to battery, and run seperate fuses for say fridge, led camp lights in roof rack, ports for chargers etc, as it's likely they will mostly be down the back anyway. 8B&S would be fine to the fuse block for the vast majority of applications.
I'd run the air compressor(s) off main battery, and generally only use it with engine running (fast idle if your model has the ability), as they draw heaps of current.
Anything external (such as Anderson plugs for camper) I would use a circuit breaker, not a fuse.
If you have a particular seperator type in mind, do a search with the function in the top left and hopefully you'll find what you're after there, as there is heaps of info on here but some may be hard to find. If that doesn't help or you have more specific questions sing out and one of us hopefully will know whatever you need to find out!