What you can do is in the xcode project, create two targets (one tweak and one application), both using iOS open dev, and then package them in the same deb. The way you would package them both is creating the correct path to the applications folder (/Applications/YourApp.app) and the path to where your tweak goes (/Library/MobileSubstrate/DynamicLibraies) in the same deb folder, and then build the folder by typing this in terminal
sudo dpkg-deb -b YourDebFolder
The folder should look like this
Where DEBIAN
contains the control file, Library
contains a subfolder named MobileSubstrate
, which then contains another subfolder DynamicLibraries
, which contains the tweak, and the Applications
folder contains the YourApp.app
file.