If you are not web programmer I doubt you will be able to modify a e-com system that does not support bitcoin to accept it.

I think the prices should be converted server-side, by fetching current trading price. There should be some kind of protection agains price spikes so it should be updated according to the period of time rather than current price snapshot.

After accepting bitcoin payment you should as soon as possible (ideally by server side scripts) exchange bitcoins to your fiat currency of choice since price can change not in your favor very fast so your original price will no longer be valid.

to do that you may want to keep enough bitcoins on the mtgox accound (or other exchange) so you can exchange immediately after purchase, and when the new bitcoins arrive to that account you'll have the same amount reserved as before. this way you won't have to wait while funds arrive by which time the price may change not in your favor.

so as you see this system is going to be rather complicated so only an experienced programmer can implement it correctly...

perhaps someone who is already accepting btc in their web shops would like to share their code to promote btc commerce.