If you've created a stamp of your signature that has a transparent background, you'd use the Stamp tool to apply it. In Acrobat 11 you access the Stamp tool by selecting: Comment > Annotations > Add Stamp (stamp icon)
I forgot to add that access to the type of e-signature you want to apply depends on how the document is set up. For example, it won't be available if the document includes any digital signature fields, is Reader-enabled, has certain security restrictions, etc. This feature has also evolved over time, and depends on which version of Acrobat/Reader you're using, so keeping track of what works and what doesn't can get confusing.
The stamp method I mentioned above is a more general approach and you can flatten the stamp after placing it so it can't be so eaily moved/resized/rotated/deleted. Post again if you'd like more information.
I too have this problem. My custom stamps that worked only a week ago now do not have a transparent background...what happened?