I'd normally be with
@mike on bringing just one bike due to the hassle of dealing with 2 bikes and risk of theft. If you are concerned about breaking something and parts availability though, a second bike is definitely an option if you don't already have spares to bring along. There are plenty of shops in those areas. If you have them I'd bring stuff that commonly breaks/needs replacement like rear D, brake pads, tire, cable, quicklinks etc, along with related tools like bleed kit and anything else you need to fix common issues. I do a ton of road trips often to areas without shops and I bring more stuff on those than when there are shops in town. It's not often I've needed to replace something but it happens occasionally, and you can never predict what might come up. Also - if you will bring the bike into your hotel, consider a tarp to lay down to keep the room clean.
When is your trip? I'd definitely do some research into rides ahead of time and have an idea of what you want to do. 2 weeks isn't a lot for those three locations. I'd also come up with alternatives in case conditions aren't good. If you're going soon any high country in Durango won't be accessible yet. Get into May/June and fire danger might shut down the forest around Flag completely, or there could be an early season fire in CO. It happens. Also look into riding and other stops along the way. Not sure if Monument Valley is open yet or whether New Mexico still has travel restrictions. If no issues, Gallup and Farmington have decent riding and MV is a necessary stop. Phils World in Cortez is fun for a few hours but I don't think hiking is allowed. Sand Canyon has hiking, riding, and cliff dwellings for the wife to check out while you ride.
For maps, you can rely on Trailforks for AZ riding.
@schillingsworth and co keep it well up to date. TF looks pretty good for Durango as well but I can see a lot of forest roads aren't shown clearly which is one of TF's big weaknesses. You'd need to get a subscription for TF to use the app via mobile, not sure if that is a big deal for you but I'd recommend it. If you like paper maps, check out Latitude40 for Durango
https://www.latitude40maps.com/. Their Telluride/Silverton/Ouray map is also worth getting as there is some great riding just off the Durango map. And you'll want to go back : ) For Mancos/Dolores/Cortez/Rico area the BigLoopMaps map is a good one, you can get it at a shop in Cortez.
https://biglooptrails.com/colorado-trails. For trail conditions around Durango this site is updated regularly:
https://www.durangotrails.org/trail-conditions/
Prescott used to produce a paper map of all trails in town for $1. Looks like it is downloadable for Avenza now.
https://www.avenzamaps.com/maps/1109013?. Avenza is worth having, it's a PDF reader for your phone that shows your location on a geo-referenced map. It's free. Not sure if Prescott still prints the maps.
Don't forget to take lots of pics for the trip report! Happy to help with questions about any specific trails.