I don't have a Shop Rite or Costco around here, so I don't know their specifics. But I can tell you what I do for Kroger who also uses ecoupons.
The sites that I use are cellfire.com, shortcuts.com and pgesaver.com. You register on each site with your store's shopper card. Then you pick the coupons to load onto your card. These coupons are manufacturer's coupons so you cannot combine a paper coupon with an ecoupon(not at Kroger anyway). Also, ecoupons do not double/triple.
Another ecoupon site I use is savingstar.com. It is a little different than the other sites. The "coupon savings" does not come off at the cash register. Instead, it goes into your savingstar account. And once you reach $5 of savings, you can cash out for different gift cards. And since the coupon doesn't come off at the cash register, you can combine the savingstar coupon with a paper coupon.
ETA: None of the sites I posted charge a fee.