Azure Domain with O365 E3

Hi,

we have a 365 E3 subscription and an Azure subscription. in our 365 we have a custom domain (say mycustomdomain.com).

now we like to join servers (Azure VM's) to our custom 365 domain (like server01.mycustomdomain.com) and use the domain services from within that server.

we have one custom domain within our 365 subscription controlled by our provider name servers and one custom domain controlled by MS name servers.

questions:

1. can we use one of the two custom domains? and if yes which one is best?
2. do we have to pay extra for activating domain services (as in create a new Azure AD Domain Services resource)? if yes, so it's not included in the E3 subscription?
   
3. if we cannot use the default or any currently in 365 existing custom domain, can users still logon on the joined servers with user@defaultdomain.com?

I have tried to get answers from documentation but i got lost. i hope someone can point me to the right direction.

thanks very much

Paul.