Hey there,
Just thought i'd donate my 2 cents worth.
Amphiprion percula and A. ocellaris have been part of major disputes. While many scientists and taxonomists think that they are indeed one and the same species (differences arising only due to differing geographic locations). Similarly, Bengal tigers and Siberian ones are technically the same species despite the obvious physical differences. A. percula generally inhabits the western pacific side while A. ocellaris inhabits the indonesian, westwards. Also many scientists and, more importantly, aquarists think that A. ocellaris and A. percula are distinct species. A. percula usually has much more distinct black rims to the bands, as well as being a brighter orange. However, this is just a guideline; many Ocellaris have bright colours (eg the one on the live aquaria catalogue) etc.
Additionally, under the percula subheading, several races have evolved: the darwin "black" perc, the "onyx" race as well as the more recognisable one. This again is due to the differing zoographic distribution of the species/subspecies. I do not doubt that within the Ocellaris Species/subspecies there are also differing variants, however, i have yet to see concrete evidence of this.
In relation to what Infidel said, there seems to be a consensus that many aquarists feel that A. ocellaris is the more aggresive of the two races. However, in my own opinion, Percs can be just as tough.
Although Ocellaris captive breeding has been greatly greatly superceeded Perc breeding, this is probably due to the higher availability of Ocellaris clowns (esp in earlier years). Now that percs are becoming more common (despite higher prices), it is likely that more and more true percs be available as captive bred specimens in the near future. Indeed, several institutions have already bred them at a commercial level (liveaquaria). It is also interesting to note that, in captive clowns i've seen, the ocellaris ones produce normal looking offspring, however, the true percs seem to produce misbanded offspring. Some sources say that the band normalise over time but i have not confirmed this myself. In any case, many find the uniqueness of the barring a novelty.
Finally, i would just like to add that; due to the more dominant nature of both clown species/subspecies, i hope you either get the chromis first, then the clown a while later; or buy a smaller clown than the chromis.
Hope all this helps.
PS, sorry to write so long a textbook on them. makes me sound like some old kook.