Here are some options:
1. Sideload: copy an apk file from your computer to the SD card of your Nook via USB. Use any file manager to access the file. One click will start an install.
2. ADB: you should have wireless ADB on your Nook after rooting with NM. Download Minimal ADB and Fast Boot
and install on your computer. Drop your apk file into the program folder and initiate an ADB connection, starting wireless ADB on your Nook first so you get the address and then connecting your computer to that address (see download link for more explanation). Once you have ADB connected, type "ADB install whatever.apk" in the console window and you're good to go.
3. Methods 1 and 2 assume you have an apk file from somewhere non-market. To install Market apps you need to do the GApps addition to NM and get your Market connection functioning. Then you can use the Search Market app to hunt down apps, or--easier maybe--browse at the Play Store on your computer. If you're logged in (same account as on your Nook) and you've successfully established an identity with the Market and your Nook then you can just install from your computer and if you've got your Nook wireless turned on the file will download and install all by itself. Like magic! (at least I
thought so the first time it happened).