I think that MS Word headers & footers are either present or they are not. I do not think you can optionally turn the on & off.
If that is true, then you will have to delete the headers and/or footers before printing on your pre-printed letterhead paper.
So now the question becomes, how can one have TWO versions of a WORD document; one with headers and footers and one without (but the content of the letter is the same). hmmm.
Optionally, you might use WORD to create your letterhead. And use plain paper when you print it and it is there when you send it electronically.