As an example, let's say the application is in the \APP subdirectory, and its data is in \APP\DATA which should be the working directory:

mount c c:\dos
cd \app\data
\app\myapp.exe

The first command mounts the emulated C: drive, the second command makes the \APP\DATA subdirectory the "working" (or current) directory, and the third command executes the application at its "target" location. Note that the working directory doesn't have to be a subdirectory of the target directory like it is in the example.

Awesome! This was a huge help. I did have to a c: after the mount c c:\dos line. Is it possible to have the working directory be on a different drive than the target location?

Yes, you just have to specify the drive letter appropriately, as in

1mount c c:\dos
2mount d d:\data
3d:
4cd data
5c:\app\myapp.exe

That worked perfectly. Last question is there a way to indicate the username dynamically as part of the location...such as mount c c:\users\%username%\appdata\local....I tried %username% but it didn't work. I'm wanting to but the data folder under each users appdata\local folder.

No, there is no (straightforward) way to use "%username%" from within DOSBox. In order to use %username%, you will have to specify the relevant lines in the Windows command prompt or the Windows shortcut when launching DOSBox, as in

1dosbox.exe -c "mount c c:\users\%username%\appdata\local" -c "c:" -c "cd data"

and so on.

P.S. Instead of using %username%, consider %appdata%.