If the flapper attachment has ears to hold the thing, you should ONLY use them. Some flapper valves have a ring around them that fits on the overflow tube and is ONLY used if there are no ears. IF you use that AND the ears when it has ears, it usually will not seal. In that case, you'd cut out the ring so only the tabs are left to engage the ears. When the handle is in its normal position, there MUST be a slight amount of slack in the chain to it or it may be holding the flapper up off of the seat, and allowing it to leak. If there's excessive amount of chain hanging down, it could be getting caught underneath the flapper...either cut it off or clip in in a loop to keep it out of the way.
If the arm on the flush handle rubs on anything, it may not move freely and the thing could get hung up. Sometimes, a slight bend is required for clearance, or move something.