I use three main colours – red, green and blue. I use red for a warning that I should not do, green for a positive statement to apply to my life and blue for verses that are nuetral.
In the attached photo from Proverbs 18 so you can see what I mean. Verse 13 is negative so it gets a red. Verse 14 is nuetral, hence blue. And verse 15 is a green positive.
When I finish I read back over the green and prayerfully ask God to help me apply these things to my life. It is a simple thing, but I find it helps me apply Scripture to my life.