padded liners are fine but i'd just as soon wear regular bike shorts then put other pants or shorts over them. the only difference i really see with the so called "liners" are that they don't come up very high on the waist so you end up having plumbers crack riding down the street if you don't have long enough jerseys on. Of course i'm 6'3" so it's getting the long jersey that is a bit of a problem.

Bib shorts solves this problem but you are talking about commuting on your bike so thats probably not a great option.