Using the new 0.6.0 JauntePE gui to make a portable app package for a basic app is now almost as simple as 1-2-3.
By way of example, we'll closely duplicate crownixx's 7-Zip Portable package. So the first thing you'll need to do is download the latest 7-Zip installer. Once that's done, and assuming you have the latest nightly build version of JauntePE up and running, the steps to making a portable app package for 7-Zip are as follows. Please note that this presents just one approach - you may prefer the wizard approach if you need some hand holding or more control.
First, select the Basic package type via the down arrow to the right of the New button. Choosing a package type in this way determines how portable the apps are that get launched via the package, as well as how portable the user data is that's created via those apps. Looking at the Isolation section of the Package tab, note that the Basic package type gives you portable App Data, Program Files, Windows, and Documents folders only.
Next, start the 7-Zip installation process by selecting App->Install via the down arrow to the right of the Add button. Browse to the downloaded 7-Zip installer executable, select it, and finally select the Open button. At that point you should see a new 7z... Portable Install entry show up in the Available Launchers list. Double click on that entry to begin portably running the 7-Zip installer. Run through the installation process as you normally would. The only thing you need to concern yourself with is that the Destination Folder is somewhere in the Program Files folder, which is what the installer should default to.
Once the portable installation has finished (note the change in package size), the final step is to create the launcher for the now portably installed 7-Zip file manager app. Do that by selecting App->Launcher->In-Package App via the down arrow to the right of the Add button. This will pop up a list of all of the executables within the portable file system. To create the launcher, double click on either the 7zFM or 7-Zip File Manager entry. And there you have it, a launcher that will portably run the 7-Zip file manager app.
To make the package permanent, select File->Save, browse to the folder you want the portable package folder stored within, type in the name of the folder, e.g., "JPE 7-Zip", and finally select the Save button. The saved package folder will contain the 7zFM launcher executable along with a JPE sub-folder containing the portable runtime, registry, and file system.
It should be noted here that this package is slightly different from crownixx's 7-Zip package. This package includes a portably stored Documents folder and his does not. crownixx also manually enhanced his package to work better on systems that have 7-Zip installed normally, in a non-portable manner.