You can get to the settings by right-clicking the window bar (why this isn't on a [gear] icon is beyond me). If you want it to take over as the default command prompt, the option you want is under Integration > Default Term, its the first checkbox.
Now, to get the MySysGit Bash to open:
- Go to Startup > Tasks
- Hit the [+] Button to create a new task
- Give it a name
- Set the task parameters to /single /Dir "[YourStartupDir]" /icon "%ProgramFiles(x86)%\Git\etc\git.ico"
- Set the shell with the command