should you use invisible thread or use color thread what do you prefer?

What kind of applique are you doing?

for most applique, hand or machine, I think you want to use a matching thread. If you want machine applique to look like hand applique then invisible thread is the way to go. Then there are times with machine applique that I like to use black or a much darker shade of the piece I am doing just to set off the applique. So I guess its safe to say you can use whatever you like!! :D

My thoughts exactly, whatever you think looks best and works for you.

i am doing machine applique and the applique is maple leaves

Well, the traditional way is to match the thread to the background fabric if you are hand sewing it on. If you are using a small zigzag, use the patch color. It you are using the iron on raw edge way, you can use the invisable or use accent color and a satin or decorative stitch.
I have been reading a couple books on this very subject the last two days. One is applique for the terrified quilter" and the other is "Applique, the basics and beyond", by Janet Pittman. The last one is my favorite and has tons of nice pictures to help you learn. (It is borrowed from my next door neighbor though) I gotta buy this book!

The point is there is many ways to do the applique. Some ways are for show. Some are for utilitarian for hard use. (as in the case of a baby quilt) The allpeoplequilt site has videos that you can watch on the subject that is very helpful.

the leaves is different colors i throught maybe using invisible thread since it is different colors ther would be to many threads.

Is there a background main color?

You can get some beautiful variegated thread that might blend in with the multi tones of the leaves :D