The Clerk of the Court may be able to help you figure things out, or you may wish to consult a local attorney about this issue. Normally, you would have to resolve the issue of paternity through the divorce proceedings, so as to have the child(ren) determined to be "no of the marriage". The affidavits should resolve the issue of paternity, such that no further court ruling is necessary; but that doesn't necessarily resolve the question of which type of divorce to file.

Either way, you will probably need to identify the children in the complaint, and request a judgment which affirms that they are not of the marriage, and thus that no custody or support issues are implicated.