After following Best in Slot's merchant tutorial every thing worked ok but when I look in the merchants inventory theres is nothing there all it says is prisoner.

if it says "prisoner" you may be using the wrong merchant chest (sounds like default player character's "conainter").

when you select the merhcant chest for the vendorservices faction of the merchant, make sure it is pointing to his chest that contains all the stuff you want him to sell

if you get it pointing to the right chest, make sure that the chest actually has sellable items according to the type of vendor the merchant is. for example, by default a blacksmith vendor will not sell soul gems even if soul gems are inside his container. he will only be able to sell blacksmith related items flagged by the appropriate keywords

I ticked the Not Sell/Buy option in factions and everything seems to be working ok now, The Merchant chest I'm using is the bits and pieces one from solitude