Problems with git submodules

I have project with root repository and some git submodules inside

Every time I have problems with buld-in git support:

1. Then I make commit I need to make commit for root repo separate. But sometimes commits for all repos make synchronous. Usually I need to open project tree, click to sync dir, got root dir blue color (changed) and after that I can commit root repo.

2. Then I merge one branch to another I got conflict on root repository. So I need to make commit for resolve this conflict 

Anyone has the same problems? Or how to organize work with submodules ?