there are NO HARD/FAST RULES!
when appliquing with multiple color fabrics choose a neutral thread color...grays blend well- light gray on light fabrics, darker gray on darker colors. you do not have to change color constantly-it's ok to use the same one throughout. taupe also blends well...i use silk thread too- it glides so nicely- but often i simply use a neutral instead of trying to match anything- it is fine enough that it is pretty close to invisible anyway. but don't stress over (Hard/fast rules) there are none! people use what works for them- they may recommend their choice- but someone else will recommend something totally different because that is their choice.