There is no "best way". My way involves documentation. Some of it is detailed and can be stored in a safe place, the other is in a quick "cheat sheet" format so you can quickly move through scenes.
When I was programming my DMX Operator(which I currently gave up on doing after getting MyDMX... but I really should go back), I did as following:
Bank would be my "grouping".
For example:
Example for Bank 1:
Scene 1: White
Scene 2: Red
Scene 3: Green
Scene 4: Blue
Scene 5: Yellow
Scene 6: Purple
Scene 7: Orange
Scene 8: Light Blue
(I could be wrong, but that's sufficient for example purposes)
So, bank 1 would be me using Gel'ed Par 38's to obtain those colors, with the Par 38's being gel'ed Red, Green, Blue and Yellow.
Bank 2 was my Color Fusions doing those colors
Bank 3 was my Chauvet Intimidator Colors doing those colors.
Bank 4 was "cans+Color Fusion"
bank 5 was Cans+Intimidators
Bank 6 was Fusions with Intimidators
Bank 7 was putting those all together.
So, I did things in what I considered logical groupings. This may not work with how you envision things, but for me, it worked because it sorted things by "type of fictures used". In fact, my way may be the absolutely stupidest thing ever compared to what you're intending to do, based on your knowledge of lighting design(mine is near none, BTW) and your fixtures.
I also built a bank of "quick scenes", which I think was my bank 1. A bunch of white washes at various intensities and fixtures just so I could quickly bring something up in between songs. But I never got a chance to use it.
My lighting addressing is done as such that my DMX addressing lines up perfectly with my DMX Operator and MyDMX, so should one fail, I'm still good to go. But, that leaves me with the problem of still needing to program my DMX Operator, which I really DO need to do.
To put it another way: If it works for you, then it's right.
Document what is in a scene by documenting your settings. SHOULD you nuke your DMX Operator 192 for whatever reason, this gets you back and running quicker. Save those in a safe place, such as in a binder inside vinyl sheet protectors. Make yourself a cheat sheet telling you what your scenes are so you can refer to them quickly. Color printers are so inexpensive, go ahead and use color to bring attention to things, like "match colors" would be good. Also keep that protected, but handy, so maybe laminate it or else have your "show binder" that has notes like this in it, and in a sheet protector. Doucment your "Chases" too. Perhaps naming them like "happy song" or "fast song" or "booty banging" or "atomic suicide death slam", "slow dance", "make-out tune" or even "DJ on potty break". Whatever works for you.
One last tip:
When programming a DMX controller, I suggest resetting it to factory detfaults before you start. This should zero any stored banks, scenes and chases. Starting with a clean slate means you won't have anything in those scenes you aren't expecting, which saves headaches with troubleshooting. This is super important when you're going to program your unit without hanging lights and seeing what you've done. I'm going to configure mine blind. This is NOT a smart thing to do.