Importing a new certificate is documented here: http://java.sun.com/j2ee/tutorial/1_3-fcs/doc/Security10.htm...
The verification of the certificate is delegated to a TrustManager[1]. Certificate paths can be checked[2] and the TrustManager is flexible enough to support a large variety of verification scenarios[3].
[1] http://docs.oracle.com/javase/1.4.2/docs/api/javax/net/ssl/T...
[2] http://www.exampledepot.com/egs/java.security.cert/ValidCert...
[3] http://stackoverflow.com/questions/11681474/how-can-i-trust-...