Hi I've got an epiphone black beauty which I'm about to fit a free way 6 way switch ala jimmy page to, I have two different types of caps but can't remember which way around they go, which goes with neck and which goes with bridge?
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As in, the capacitors for the tone pots?
I'm not sure what you mean by "types," but i'll assume you mean the values.
There is no set way to do this, it's all about personal preference. Larger valued capacitors will cut more treble, leaving the sound darker when your tone pot is at "0". A smaller valued capacitor will not leave the sound as dark as it cuts less treble, but you get more control.
At "10", they will do very little, and I doubt you will hear any difference. So it all comes down to what happens as you reduce the tone to 0:

High value cap: More range, less precise
Low value cap: Less range, but more fine-tuned.

So if you like more control over your neck pickup, use the lower value for that. If your bridge pickup is very bright and needs "taming", use the high value for that.
Its all personal preference.