When I click a Unsigned Signature Field, a Sign Document dialog box will appear, Some of certificates in my windows cert store will shown in Sign As list, but also some of them are not, So what is the principle to select certificate? What is the certificate filter mechanism?
Each certificate belongs to a person. Generally, a signing certificates contains information identifying this person. If you procured certificates from a reputable Certificate Authority (CA), the identity of the certificate's owner is guaranteed. If your certificates are self-signed (you or someone else created them in Acrobat) the identification information in these certificates is arbitrary and does not prove anything. It may, though, convey some information about the certificate's owner, like email and name, and it is up to you to trust it or not. If you go to Edit->Preferences->Signatures->Digital IDs&Trusted Identities->More..., select a Digital ID in the left pane and click on the "Certificate Details" tab on the top of the right pane, you'll get this certificates details. Click on the "Subject" field and it will show you some of the identifying information. Self-Signed certificates have the same Subject and Issuer. Certificates issued by a CA have different Subject and Issuer.
The bottom line is if you have several signing certificates you select the one with identifying information that you want the recipient of the document to see. Of course, if this is a self-signed certificate, the recipient needs to trust the identity of the signer, which can be accomplished with a phone call, for instance.