The bifurcation of sources.list into sources.list.d/debian.list, sources.list.d/mepis.list, and sources.list/d/opera.list has confused me even more.
The thing to know is that a sources.list is a sources.list. No matter what the label is.
All are in etc/apt/
If it confuses you, all are in one etc/apt/ Folder. The wiki has a decent explanation of how to replace or modify things there and will work. Put sources.list in the Search box and hit Enter. Up will come a list of the different versions that we support. Click on the version that you are running. Follow the directions you find there. It's basically a Copy&Paste operation for the various MX sources.list containers. Or you can use Synaptic, though that's a bad use of time to my mind.
Things like the Opera repository will be in the same place. As can the virtualbox repository. These two programs, for instance, will place their repositories correctly. You don't need to worry about them. Many do not keep them enabled (using Synaptic) by default. Though it does make checking on security upgrades a manual process in that you need to remember to enable them before doing a Reload.
Yes, even I am dishonest. Not in many ways, but in some. Forty-one, I think it is.