OK jimmer, here's how you do it.
You need to make the logo into a drawing object (will come back to this in a min). First, go to File > Page Setup. Select the Paper tab and click on the Printing Options button. There's a panel called Include with Document. You need to deselect the Drawing Objects check box then click OK. Click OK on the Page Setup window to close it.
Now then. This bit depends on what format your logo is - I'm assuming you have it as a graphic file somewhere and its been inserted into the Word doc. I've just played about with this and it works. Delete the logo from the page (making sure you have the source file - jpg or whatever - elsewhere). Select Insert > Picture > New Drawing. This creates a drawing frame. Then (and this is the tricky bit) you need to make sure the DRAWING FRAME is selected, then click Insert > Picture > From File. Browse to wherever your source graphic file is, and select it. The picture will be inserted into the drawing frame as a drawing object, not as a normal picture (which would happen if the drawing frame was not selected first).
To check that it has all worked, go to File > Print Preview. The picture will be absent from the print preview.
You will need to do this on the master template so that all docs to be sent to customers have the same page setup (without you having to go through this with each one!).
Any probs, let me know ;-)