Until you have done a dozen or so batches figuring out the best system for you, Read books, talk to your LHBS, comb this forum and a couple others for whatever question you have. If you run into an anomaly, such as your LHBS giving you a line of BS like they did, then you know you can discard it.
However, don't bottle from your carboy. Spend $10 on a bottling bucket like the one in Revvy's thread and save yourself a TON of aggravation.
My opinion about the clarity is thus: There is NO difference save for the time it is left undisturbed. If you primary for 6 weeks, it will not be the same as primary for 3 weeks, secondary for 3 weeks because in the middle of the settling you have disturbed it increasing the time it takes to become as clear as leaving it undisturbed for 6 weeks.
Me, I don't care about clarity especially since I know, in my system, enough time in the bottle and refrigerator yields me commercial clear beer for most batches.