Version control directory vs workspace directory

This confuses me forever.  

I thought that is was always better to have different locations for where you have the code checked out/cloned, compared to where you have the IDE workspace for your code.   Following are just examples:

c:\\mydata\git\<project>

c:\\myapps\intellij\workspaces\<project>

Every time I try and set things up like this the IDE gets confused.  I have successfully done this using eclipse, but always forget exactly which hoops I jumped through.

Should I just give up on this, and use the same directory for both - which I do understand can also work.

Thanks