You collaborate on sites' code using Git. If you're not familiar with it, you need to become familiar. And not just for this project. It is an awesome program, and you should use it to track changes in all of your development projects, regardless of whether or not you work on a team.
I wrote a guide on getting started with git if you have little or no experience with it.
All the projects are actually Git submodules within Sapwood's
projects directory. This is because sapwood itself is a Git repository.
Creating And Importing
It's important you following the guide to creating and importing, which essentially means you need to create or bring the project repo on to your machine via the app's interface (not on the command line).
There is a way to deploy changes you've made without logging into the server. In site settings, there is an "Update Repo" option which will pull the code and go through a server reset. It can be run in development, but it's most useful in deploying the code to production. In development, you should use the command line to pull your repo.