The best way to do this is to have each location's Echo devices on their own Amazon account.
For example:
House 1: All Echo devices in this house will be on Bob's Amazon account. All smart devices will be set up on Bob's account and linked to Alexa with Bob's accounts. This includes light switches, garage openers, thermostats, alarm systems, smart plugs, etc.
House 2: All Echo devices will be on Larry's Amazon account. Same deal as above.
If you walk into house 1 and say turn on kitchen light, the kitchen light in house 1 will turn on. Since everything in house 1 is only setup with Bob's account, nothing in house 2 will be affected by any Echo device in house 1.