Yes; but I don’t always get the Place Initials choice.
Very odd behavior. As a test, create a Digital ID file and remember the password. Then that prompt should no longer occur when you try to use the Fill & Sign Tools. If it does then you may want to consider reinstalling the application.
You want to use "Place Signature" (shown in Steve Cordero Mar 17, 2015 11:31 AM reply), not "Sign with certificate". When you first click on "Place Signature" you get a dialog to select the signing method. Acrobat remembers it and present the same saved signing method when you click on the "Place Signature" the next time. It is possible that you selected "Use a certificate" the first time and Acrobat remembered it.
After the first time the "Place Signature" button has a small triangle next to it on the right. If you click it, you get the choice to change "Saved signature". If you select it you are presented again with the dialog to select the signing method, at which time you can choose "Use image".