I went with a Burris 3-9x40 for my encore (th). My question is ring size. I'm about to order the Warne base...but would you recommend low or medium rings (QD Warne's as well)? I would love to leave the rear sight on but would rather have a scope properly fitted to the gun. Thoughts???

Take the open sight off you will never use it. I have a Savage 10MLII with Warne QD rings and I have a 3x9x40 Bushnell on it. I had to go with the medium Warne mounts.
Chap

take the rings off they will get in the way of your scope since you will have to move it a bit forward. plus you'll not use the sights since you havea scope on it. if you plan on using your sights in a state that doesn't allow scopes, (which may be why our using QD style rings) just put your irons back on. otherwise I'd with with a Burris sig weaver style rings.

I have a 3x9x40 swift on mine and a 1x32 T C that I use in WI muzzy season I se leupould mid mounts and switch back and forth.