For managing USB files, Hekate is the best tool for the job. You do not install Hekate, in fact its impossible to install it because its a payload so it only ever runs in memory meaning that once you exit Hekate, you will need to resend Hekate in order to use Hekate again.
For installing files via USB, I use a homebrew program that you didn't mention which is
TinWoo Installer. Its what I've always personally used and recommend to new users because I've never ever had any issues while using it. Of course, when it comes to USB installation, you need a PC program to push the files via USB which can be accomplished with NS-USBLoader.
The simplest fix would be to have 2 separate Nintendo folders; one for emuMMC and one for sysMMC. Make a copy of your current Nintendo folder and place it anywhere else on your SD card except the root. An easy place to put it is inside your emummc folder. Then change the emmc.ini file to point the Nintendo folder to where you put the copy.