I'm interested in buying a Cole Clark, and had a question.

Does the FL1AC have a lower acoustic quality that the FL1? Or is there no difference? I'm interested in an Acoustic guitar, and being able to plug it into an amp would be nice, but not if sound quality suffers etc.

They are basically identical. The FL1AC has a cutaway which will change the tone a little (not necessarily in a bad way though, its just different) but the actual construction and the woods used are all the same (actually, The woods on the Cole Clark's varies alot, which I think is a good thing, but it may make it harder to compare side by side, but if they used the same combination of woods, then they should sound similar) then the sound should stay fairly consistent, you just pay more for the cutaway and the electronics.
hey mate, i own a FL1AC and it is an awesome guitar. ive played normal FL1s and the sound quality is the same, just with the cutaway it can be slightly different. i would seriously recomend buying it!! my FL1AC is better playing then some guitars ten time its price.
Impossible to give a definitive answer since even guitars made with the same woods are going to sound different. The cutaway will decrease the resonance area and affect the tone somewhat.
Generally when comapring standard acoustics with their electric/acoustic counterparts i find the standard acoustic is slightly better tonewise but every now and again its the opposite, it just varies from guitar to guitar.
If you do plan on playing plugged in alot I do recommend you get the FL1A or FL1AC as I highly rate the electronics in them and think they are worth the money.