mounting a hard drive should be possible with the -hard1 option (or 2 or 3). You must use the HFDC disk controller because the other available controllers do not have hard disk support. The device name is WDS1 for the TI systems and HDS1 for the Geneve. So in TI BASIC you should be able to do a SAVE WDS1.SAMPLEPRG or OLD WDS1.SAMPLEPRG. You can create subdirectories with a disk manager; I suggest the Myarc Disk Manager 1.5 (on disk). You can use them like this: OLD WDS1.SOMEDIR.ONEDEEPER.FILE
As for the Joystick 2 I just found that I cannot get input from it. So that may be an issue to be fixed.