this may seem like a simple question, can I and how do i clone an existing repository for a new project, without changing / effecting that existing project?

I have two starter projects that I use as templates both include a few submodules, When I start a new project I'd like to clone that repository, and then get going with in my new repo with beanstalk or bitBuket.

any help would be appreciated.

note : 

* I'm not a terminal pro so.....
* I use Tower for Git repo management with beanstalk and bitBucket

EDIT : 

I'd be happy to take a crack at this with terminal if thats the way it needs to be done, to clarify my objective - I need to : 

* clone a local repository
* initialize its submodules
* share it with my team via bitbucket or beanstalk (ideally the second)

from whats been posted essentially I need to mimic the fork functionality and then be able to push that to one of the services mentioned.