Sorry Ben, (and before I satrt I know my posts are often full of spelling mistatkes and typos) But a little punctuation here and there makes it a lot easier to read.
I think from what you are saying you are describing the front wheel arches where there is a metal frame that the mudgard is bolted to. If this is the case teh arch moves with the wheel so even if there is little clearance you are OK (as long as there is some clearence)
If you are talking about the rear arches, these are fastned to the frame and the wheel will ground out on them if you don't give enougth clearence. If you want to have the rear arches sitting lower down (you may if you have smaller wheels) then you need to chop out some of the arch to give clearance for the top arm of the suspension to move without touching the wheel arch.
I hope this makes sence, and helps.
Simon