I just put 'em in the seat, no cover. We owned a cart cover once and I never, not even ONCE, remembered to take it into the store. I use rings to attach a few toys to the bars to keep DS busy.
BTW, if you want to sit them in the seat more securely, I bought a nitfy padded velcro strap thingy on Amazon (called the "Anywhere Safety Strap") when DS was about 5 months old and we use it alot -- it really helped him stay upright when he was just learning to sit, and you don't have to mess with broken straps that are on many carts. PLUS it keeps him from leaning down far enough to get his mouth directly ON the cart.
