I do not understand the question. Which options have you not selected? What do you mean by "the document will not work"? Why do you need to remove "trusted certificate"? Usually you need to add a trusted certificate. There are cases when existing trusted certificates do not do what you want but such cases are rare and usually happen in IT-controlled environments.
I presume that you have a signed PDF and want to validate the signature. You do not validate certificates separately. This happens as a step in the signature validation. You may get signature status "Unknown" because the signature's signing certificate does not chain up to trusted root. You can check that by right-clicking the signature and selecting "Show Signature Properties"and then "Show Signer's Certificate". A certificate Viewer dialog comes up. In its left panel it shows the certificate chain. You can check the trust by selecting each certificate in the chain and clicking on the "Trust"button on the top of the right panel. In the "Trust"pane there is a button to Add selected certificate to "Trusted Certificates". Usually trust is assigned to the top certificate in the chain (root certificate). Be very careful by assigning trust to a certificate. Be very sure that you know what you're doing and that you really trust the issuer of this certificate. If you assign trust to a wrong certificate you may get spoofed signatures marked as valid.
You can manage your trusted certificates by going to Edit->Properties->Signatures->Identities&Trusted Certificates->More and selected "Trusted Certificates" in the left panel. The right panel will contain list of the trusted certificates in your Acrobat/Reader installation. On the top you'll find tabs that perform various actions when you select a certificate in the list.
You may want to educate yourself by reading documentation and tutorials on Digital Signatures in Acrobat. Google will find many of those for you.