Problem with permissions

We adding new domains and installing them using SSH from another server. We came across a permissions problem. A new user and group are added to each domain. Logging in to it is impossible because of the SSH key to the Git (in that case you should add the key to the bit bucket from time to time). Data manipulation by logging in to another user (root type) changes domain file permissions which may be related to incorrect operation of the page.

Was it possible to use one user for all domains?
Probably we could use “child domains” but will it be safe to raise the privileges for this user?

Thank you in advance for any single suggestion.