I'm gonna try and explain this as best I can. If it confuses you further I apologize.
Modifiers are used as shift keys. You use them to change what your MIDI controller commands do.
So, for example, you are using a standard VCI-100, set up like any other controller. You want to make your transport buttons (Play/CuePause/CuePlay/Cue) control your loops instead. So you create a modifier. M1V1. You create four commands on those same four buttons (Loop Size Up/Loop Size Down/Set Loop/Reloop). You set them to M1V1. Now, whenever the button you assigned for Modifier 1 Value 1 is active, those buttons control your loops. Now, you need to tell it that the transport buttons should not work on M1V1, so the default is M1V0. Whenever no modifiers are set, those buttons will work as transport buttons.
Now, this is where the logic of modifiers comes in on a personal level. You can designate individual Modifier numbers for individual functions. So, M1V1-7 will be different modifiers for loops only. So, M1V1 will set loop size and drop it, M1V2 will set custom loop sizes (Set Cue In/Set Cue Out/Loop Move Fine Up/Down). Now you will want to switch between them, so you set a command to set M1V2, depending on the function you are going for at the time.
Now, you want to augment your controls even more. You can't have controls set to M1V1 AND M1V2 at the same time. It just doesn't work. Modifier 1 can't have two different values at once. So you want to have four deck control on your two deck solution. You create M2V1. When M2V1 is active then you control Decks C & D. Now, you go through and set all of your commands that change (EQ, Volume Fader, Transport, etc.) to M2V0 for A/B and M2V1 for C/D. Now, this is where things get big.
You have your transport buttons set to M1V0 already. Now, you set them to M1V0 M2V0 to control A/B, and then M1V0 M2V1 to control C/D. But you want those same loop functions for the other decks. So now, when M1V1 M2V1 is set Loop Size Up/Loop Size Down/Set Loop/Reloop works on decks C/D also. You wouldn't be able to do this with only 1 Modifier with 7 values without a LOT more being put into your .tsi. And, at that, you have 8 Modifiers with 8 values (0-7). That leaves... a lot of different modifier combinations to play with, making any controller completely individualised based on the individual DJs needs.
I don't know if this helped at all, though. If it didn't, sorry :-)
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