You will need to figure-out you iDOS 2's directory using a file-manager.
The location will be something like this:
"/var/mobile/Containers/Data/Application/????????-????-????-????-????????????".
Within this directory, place DOS software inside of "Documents/apps".
The 'iDOS 2' configs are inside of "config/default" as the files 
"dospad.cfg" and "ui.cfg". The "dospad.cfg" behaves like DOSBox's
config file with an "[autoexec]" area at the bottom, to which is used
to launch the PLAY.BAT file you would have seen during navigation.
The 'FileBrowser' program from the BigBoss repository, installed using 
Cydia, can be used to edit these files via the "(i)" icon.