Omega theme and sub sites sub theme

Is this scenario possible with Omega responsive theme?

I have several sites and they use same main theme that is located /sites/all/themes/my-main-theme. This theme is based on Omega responsive theme, so I also have /sites/all/themes/omega theme.

Some sub sites have some changes to main theme. So can I use my-main-theme and just do some small changes to one or two templates and css file on my sub page? So that www.domain2.com would use most theme files from /sites/all/themes/my-main-theme but also one template and CSS file from /sites/domain2/themes/my-sub-theme

Is this possible with Omega? I tried something like that but www.domain2.com site lost all themes then. I might have done something wrong there though. Thanks!