I use the closest slot for my Big Stopper (it's got foam light sealing, which makes it thicker than the normal filters), but for that I had to reverse the pins that hold the adapter ring so that they can be flush with the outer face of the filter holder, otherwise they'd scracth the foam and maybe even the filter.
At length, yes, you can only use the two outermost slots; which, in a sense, it's fine, since too many filters in front of your lens would degrade the picture quality. There might be a way for you to buy the parts to add a new slot: the screws look long enough to accept just one more piece. You'd have to check Cokin's web site and documentation to see if this is a viable option.