The way snippetmaster works is that each User is limited to the "Starting Folder" that you specify for that user. The User can navigate "down" into that folder, but not "up".
So if you have created a user with a Starting Folder of "domain 1/public_html/", then they will not be able to navigate "up" into the "domain1/" folder.
To see how "Starting Folder" works, please login as admin, click the admin link, then Users tab. Now click to modify a user, and put your mouse over the "?" icon next to the "Starting Folder" field. A popup will explain what this setting is for.
So.. what I recommend in your situation is to create two Users.
User 1 can have starting folder of "domain 1/public_html/".
User 2 can have starting folder of "domain 2/public_html/".
You login as User 1 when you want to edit "domain1.com". You login as User 2 when you want to edit "domain2.com".
I hope that makes sense?
>> Is there a printable snippetmaster user manual?
No. There is only the online manual here: http://www.snippetmaster.com/documentation