I can see that I'm way out of my depth on this one. Could someone explain the basic set up, just so I can start to build up an understanding of how these things work
The way I have done mine is I have got a 120amp relay between the two positive terminals, this is switched via an ignition live (many people will use the alternator output to switch this so they are only connected whilst the engine is running, I prefer it on ignition live as this will allow the second battery to back charge the first if its a bit low and wont start the engine, personal choice though). I have then got a 60 amp cable on a 50 amp MAXI fuse that runs up to the dash area, this is then served via a distribution block to each electrical item with an inline fuse rated to whatever is plugged in. I will shortly be changing this to a secondary fusebox to tidy up the wiring as inline fuses means lots of wires everywhere.
As for switched items (lights, winch relay e.t.c.) I use relays inline in the main circuit that is then switched via providing the relay with an earth, this keeps down the number of live wires running around the vehicle (these earths will become live when switched so same care is to be given). This isnt always needed, if your wiring runs through the dash anyway then just switch it.
As has been said the correct wire ratings need to be found, to find correct amp of ratings you need to total up the wattage of devices in that circuit, devide by the voltage so an example would be 4x55w lights would be 220/12 = 18.33 amps, I personally would over rate a wire so for that instance I would use a 25 or 30 amp cable (depending what you have to hand) and would run a 20amp fuse. In this case I would use the relay switching system as a 25amp cable is a big cable to be running all over the place.
You also need to make sure all connections are good and strong, crimps are fine if done correctly (if its lose the wires will fall out with the slightest pull), do not use scothc locks and choc blocs are OK but prone to corrosion. DO NOT TWIST AND TAPE, I see so many 'connections' like this (just like the previous owner of mine when he done the headlights

)
And earths, you can earth just about anywhere but make sure the connections are good, no paint e.t.c. Some devices can be sensitive with sharing earths and can lead to fluctuations in operation so be wary.
I'm in the middle of makingnTwin battery tray and going to fit a split charge system, my local motif spairs place have git me a waterproof split charge relay, I know how to wire it up ect, my question is, my battery's are both going to be 85ah 1000cca
I know if these are wired in parallel I will get 170ah that makes for good winching,
With a split charge relay will I still get the extra kick from the second, if not is there a way round it, without spending a fortune on a mega fancy mega priced split charge system?
The main point of the second separate battery for winching is that you don't run down your main battery for starting and running the vehicle. Use them both when winching and you stand a real chance of being stranded without battery power .. a winch will take all the power you can give it, it really doesn't care if it flattens both batteries!
As paul said the split charge should split the batteries. You can simply run another battery in parallel without any splits systems and it would work but it would be like haveing 1 big battery. Some people have a manual switch so when whinching with engine off they can isolate a battery. A decent 1000CCA battery will cope alone with a winch. AH aren't really of concern here (unless your doing alot of winching), its about how many amps you can put out quickly (CCA = Cold Cranking Amps, how many amps can be put out instantly at a set cold temperature)