Which version of rxTools are you using? Does it use rxTools.dat or code.bin?
Here are some launcher links that should work, depending on which version of rxTools you are using:
https://dukesrg.github.io/?rxTools/sys/code.bin
http://www.reboot.ms/3ds/load.html?rxTools.dat
Edit: The currently active fork of rxTools can be found here:
https://github.com/dukesrg/rxTools. It has instructions on how to use it with MSET with either a DS flashcart or browser.
Don't feel like you have to update just because everyone else says to. Start with what you know. Research what has changed since the last time you checked the scene. Move forward only when you want to and have the knowledge to do so without screwing up your current setup.
One thing that you'll need to do before updating is backing up all of your save data. I would recommend using JKSM, as it's more user-friendly than SDF. Part 5 of this guide will explain why you'd need to backup your saves.
http://gbatemp.net/threads/guide-the-emunand-save-data-mega-guide-gbatemp-doesnt-deserve.378491/