Hmm, Lots of advise, I may as well throw some more goodies onto this thread:
1) HoneyWell 322 zone panel will do just fine if all you want is one zone = low, 2 zones = high (can do this both with heat and AC).
2) Bypass is determined by need of airflow. A "WAG" (wild a** guess) would be 10" or 12"... however it is determined by airflow. A manual J determines the amount of BTU's (heat) needing to be added in the winter and removed in the summer. When this is done room by room, the size of duct and vent size to each room can be calculated. This and ONLY THIS will provide proper ductwork. Without proper ductwork, ANY new install is a hit/miss as to whether it will work properly or not. NOW do you see why Man J is a good idea?
3) What the Rheem guy did with his cell phone is a Rheem proprietary app called 'DesignStar' (I have it on my laptop). Problem with it is; it is dependent on county records... which are usually not accurate, AND, it has a lot of variables which the user has to set up... set it up wrong and it spits out the wrong numbers. A proper Man J load calc is a good idea.
4) Two systems are ALWAYS better than one big zoned system if comfort is important. If one only cares about hot and cold air, well then all these details are moot.
5) Thermostats: The Nest 'learns' by sensing when you walk in front of it... If it is mounted in high traffic, it learns your behavior... if it is behind a door, it is worthless. The HoneyWell 322 zoneboard will work just fine with any 1H/1C thermostat... I prefer t-stats which have a common wire so they are powered and not dependent on batteries.
6) How to tell if a contractor is good: Talk to your friends and family and get referrals. Would you personally refer someone to your friend or brother/sister who made a mess of your house? Of course not. After you have a 'short list' of 3-5 contractors, check them for license and insurance. ONLY the ones who pass this test get to come out to your home. Next listen to what they say and answer their questions... they should be asking lots of questions as to what you want and need, and what issues you have. If they do not... well fire them.
The one contractor your gut feeling says is competent, has the technical know how, really CARES about the details, is respectful to YOU, and someone you would not hesitate to refer to your friends/family... is the one you probably should choose for your home.
Probably will not be the least nor the most expensive one.
Let us know how this works out.