If you have color synesthesia, and corresponding colors (for candles, herbs, etc.) don't match up, that's okay! Use whichever feels right for you. If you prefer to use the usual colors, go for it! If you're like me, however, you may want to use the ones you associate them with, which is fine too.
When creating sigils, I usually draw them in the color I want the outcome to be. While I don't do this for painting runes, I imagine that it would be perfectly fine to do so. When making poppets, I do this when I have the right color fabric at hand. Just adding colors to spells may prove helpful on your part.
If you have other types of synesthesia, it may be a bit tricky to do this. If you include the texture of something, the taste of something, the sound of something, etc. in your spells, it may be helpful.
If you have synesthesia but don't want to do this, that's alright! This isn't mandatory for spells. And if you don't have it, feel free to use the set colors.