I use the corner tags a lot. For example, if a clue indicates that one suspect is a criminal and the other is innocent, I'll tag the clue and both suspects the same color. I find it makes it easier to account for the number of criminals/innocents on the egdes and who neighbor other suspects.

Use the color toggles. You can hold right click to get the list, then just use orange for one group, pink for another, etc.

It's not gonna be helpful advice, exactly, but I just remember them. Sometimes I'll forget, but it usually works out well enough.

Corner color for iff, memory for if

Colors in pairs, all yellow are the same and all red are opposite, and so on (all blues the same blue-all orange opposite, etc.)

I only add the color if it encodes completely one or more rule so I can dim them.

If there are long branching paths, I often use screenshots and then compare.

What I do is mark in the top right with the colours (mainly just green, red and orange but you do have more colours by holding down). Then I will screenshot each combination of branch and normally there will be something the same or to rule out.

Another tip is you can get more colours by holding down the bottom right corner, so each suspect can have two different colours.