PNDStore is simply an automatic download/install tool, you won't need to open any of your PND files with it. If you would like a download/install tool that can also launch your applications, definitely try out PNDManager. B-Zar has put a lot of time into polishing it and making it both powerful and user friendly.
You should perhaps take a second to look over some of the more basic manuals on the wiki (
like this one) to understand more about the PND system.
I'll include the basics here, though. PND files (ex the download button
here gives you "qjoypad.pnd") can be placed into one of four folders on your SD card:
<SD>/pandora/apps/ - App will appear both on Xfce Desktop & Pandora Menu (this is the 'both' option in PNDManager)
<SD>/pandora/desktop/ - App will appear on Xfce Desktop
<SD>/pandora/menu/ - App will appear in Pandora Menu
<SD>/pandora/mmenu/ - App will appear in MiniMenu ONLY (note: apps will appear in MiniMenu no matter which folder you choose)
PNDStore and PNDManager simply give an easy to use interface on your Pandora that will download and place the the PND files into the proper folder for you. You can easily perform this action for yourself if you have already downloaded the file. Simply put the PND into the folder of your choice and then run it from the location at which the app appears.
For example, since you already downloaded QJoyPad, if you place "qjoypad.pnd" into /pandora/desktop/ on your SD card, then you simply need to double click the icon that will appear on the XFCE desktop to run it. No entering PNDStore or PNDManager is necessary. Those programs just make finding, installing, removing, and updating apps more user friendly. A nice feature about the PND system: if you place files into the folders yourself, programs like PNDManager will be able to recognize this and treat them exactly if they were installed by the program itself.
So, anytime you find a random ".pnd" file you would like to run, just put it into whichever of those four folders you prefer, and it will appear in the appropriate location for you to execute the app.
(With how apps like PNDManager and PNDStore have matured, the usefulness of installing yourself has become somewhat limited: test PNDs that devs will upload on the forum, or an old PND that is maintained outside of the repo. Anything on the repo can be more easily downloaded and installed directly on a pandora with internet access by running PNDStore or PNDManager.)