To sign an InfoPath form (XML) Digital Certificates need to be issued to each user in your organization using the Certificate Authority app. When you sign form templates (XSNs) for use in Full Trust forms, you sign the XSN with a code-signing certificate that you generate on a machine or buy from a secure certificate vendor, like Godaddy. The certificates generated locally on a machine aren't secure.
I'm not sure which one you are doing. I'm assuming when you say "form" you mean XSNs. I'm further guessing that you are using machine-generated certificates to sign the XSNs and this is causing popups because the machine-generated local certificates aren't meant to be used in a network scenario. If my guesses are right, you should be able to just purchase code-sign certificates from GoDaddy or some place and use those. You'll need to register them but then people who are in your domain or trust your domain won't see popups.
On the other hand, if you are using digital signatures in your form and having people sign the form with their personal certificates, but you don't want to issue separate certificates per user, then you should be looking at Electronic Signatures and not Digital Signatures. Electronic Signatures are simpler to use than Digital Signatures (pro) but they aren't as secure as digital signatures. However, for all intents and purposes, they are good enough in most scenarios (government-regulated industries requiring Part 11 compliance are one example where they are not good enough). Check out Mel Balsamo's blog on how an Electronic Signature can be added to your InfoPath form: http://www.infopathdev.com/blogs/mel_balsamo/archive/2009/03/03/electronic-signature-template-part.aspx
Good luck!