You can sign the appserv-jwsacc.jar file manually any time after you have installed the Enterprise Server. Copy the unsigned file from as-install/lib to a different working directory and use the jarsigner command provided with the JDK to create a signed version of exactly the same name using your certificate. Then manually copy the signed file into domain-dir/java-web-start. From then on, the Enterprise Server serves the JAR file signed with your certificate whenever a Java Web Start request asks that domain for the appserv-jwsacc.jar file. Note that you can sign each domain's appserv-jwsacc.jar file differently.
Remember that if you create a new domain and do not sign appserv-jwsacc.jar manually for that domain, the Enterprise Server creates an auto-signed version of it for use by the new domain. Also, if you create a domain-specific signed appserv-jwsacc.jar, delete the domain, and then create a new domain with the same name as the just-deleted domain, the Enterprise Server does not remember the earlier signed appserv-jwsacc.jar. You must recreate the manually signed version.