I ad eps logos, tifs, and even text all the time on top of PDF's using InDesign, and never have had an issue doing so. Thats what a page layout application is supposed to do.
That being said there is a few ways to ad it to the PDF using Acrobat. Opening the eps using Acrobat creates a PDF and you can copy paste it in. You could also use the ad watermark function.
If you have a tiff - or an eps, or a PDF - you can create a stamp and then place that onto any PDF - with the added benifit of scale and setting a level of transparency.
Under the Comments menu, select Commenting Tools, then cascade select Stamps, then cascade select Create custom stamp - select you image and stamp away !
Once a stamp is placed, of course it can be re-positioned and such ---