Two things to be concerned about:
1.) Make sure you're not reading data that you haven't put into the appvar.  Don't assume that the appvar starts filled with zeros, because it most likely isn't.
2.) Make sure the appvar is big enough for your purpose.  If you're using more data that the appvar can hold, it'll likely lead to an eventual RAM Clear.
Good luck!

I haven't figured out how to store a program into an appvar yet though.

For this, you'll have to make the appvar big enough and then use the copy command.  Alternatively, you could just change a program directly into an appvar just by changing the type byte.

Alternatively, you could just change a program directly into an appvar just by changing the type byte.

Sorry, but I am unfamiliar with this, could you explain a bit?

How do you create your app var?

I did...

Unarchive "appvarName"
!If
GetCalc("appvarName",4)->A
Else
GetCalc("appvarName")->A
End

yes, I realize this could be optimized, but I was testing appvars to see if i could use them like a list, and that seems to have failed, although I bet I just did something wrong.

EDIT: I tried the copy function to save a program into an appvar, then the appvar into another program (just to try both cases), but then I couldn't run the new program. Is Copy(Y1,A,size) the way I'm supposed to do it, where Y1 is the source, and A is the new program/appvar that I'm storing the data into?