The key advantage to Liberty is that there's a lot more room to share with both motorists and cyclists. Penn is narrow and steeper, Liberty is wider and longer.
As for the bike itself - yes, it's normal for the chain to sometimes rub on the front derailleur cage, especially if you're using a combination of gears that is at the extreme opposite range, ie, the big chainwheel in the front and the big cog in the back. Use of those combinations is discouraged as it places much higher stress on the chain and the gears, causing them to wear faster and wasting precious human energy. But even other combinations will sometimes rub a bit, so you "trim" the front derailleur until the rub goes away.
With traditional (old-fashioned) friction shifters, in order to get the chain to change gears, you would "over-shift" slightly and then come back to the proper position. Nowadays, that is built in to the clickety shifter mechanism, but it doesn't always work right, and it's sensitive to adjustment. You should find some threaded barrel adjusters inline with the cables, usually at the shifter, on the derailleur, or at some intermediate mounting point on the bicycle. If you turn these in one direction, you increase the tension on the cable relative to the housing, and the other way decreases it. Or to think of it another way, the adjusters move the derailleur's rest position in and out. I'd say this is like "fine tuning" on your TV, but I haven't seen a TV with an analog tuner in a hundred years.
As for the brakes, you probably need to center them, but it's a harder thing to describe all the possible variations of brake posts and nuts and washers and crap.
Somebody really needs to offer "new to cycling" or "return to cycling" classes. Hm.
