Create a folder in your SD card for these .apk backups. Example: I have a folder in my SD card called "Backups".
What you do now is go to /system/app. You should see all your .apk files there. For anything you want to remove, just check it off and delete it. If you want to back it up, copy it and paste it to your backup folder. When you want that app again, just copy and paste it back into /system/app. Reboot if necessary.
Be sure that you have root function enabled. You do that by hitting Menu > Setup > Enable ROOT function. Obviously, this whole process (except for creating a folder in your SD card) requires root.
Also, going into /system should ask you if you want to go into R/W mode (read/write mode). You need to enable that if you want to delete anything. If it doesn't ask you, you can always hit Menu > Switch System R/W. That should do the trick.
If you actually read through my long post, then here's another solution. Use Titanium Backup and select your apps to backup, remove, and/or restore.
Device: Nexus 4 (4.2.2)