I've done this mock up with cardboard just waiting for the wood to be cut, I've got quite a large amp, but wheres the best place for it to go?

Well your sub will be going down into the spare well, so put the amp by the side, under the wood, or put it behind the rear door card.

spacer the wood up so that you can fit the amp and have its top flush with the new floor

on my 6n i just put it under the false floor beside the sub, fitted koay, thats if you have enough room

You don't need much room mate to fit an amp, should be fine to go under the floor as the floor will be raised anyway for the sub

I've got it sorted, its been screwed to the back of the seat, its out the way and all the wires will filter down into the wheel well

i cant get the sub flush to the wood because the sub will be screwed onto the wood and i didnt get thick enough wood for it to be rabbeted down (if thats the correct terminology, I'm no chippy)