No it's actually a pretty easy system. I went to ship a set of tail lights a while ago, had them all boxed up so I got a UPS online quote of $35, so I went to the UPS store to ship it and the lady said it'll be $78, I asked her about it and she gave me some lame excuse, so I asked if I get the preprinted label on the box can I drop it off here? She said yes so I went back to my desk, paid for it online (yes you have to set up an account, only takes a few minutes though), paid $35, printed out the UPS label, took the box and label to the UPS store, they handed me a bag that you slip the label into, seal it and stick onto the box...and that was it.
UPS stores, FedEx Kinkos (soon to be Fed Ex Office), or any kind of store that isn't a UPS/FedEx location that has thier huge delivery trucks are basically chain/franchise locations which are all independantly owned and operated, so they have overhead costs for thier locations etc so they have a markup in thier pricing.
That's why you're getting a totally different price at the store than the online quote.