Put the certificates to the /etc/pki as suggested by:
http://fedoraproject.org/wiki/PackagingDrafts/Certificates
Nessus2 package in Fedora is using the same.


diff -ru openvas-manager-3.0.1/CMakeLists.txt openvas-manager-3.0.1.new/CMakeLists.txt
--- openvas-manager-3.0.1/CMakeLists.txt	2012-04-25 09:09:02.000000000 +0200
+++ openvas-manager-3.0.1.new/CMakeLists.txt	2012-05-11 01:52:54.527421733 +0200
@@ -155,12 +155,13 @@
 set (OPENVAS_SYSCONF_DIR  "${SYSCONFDIR}/openvas")
 set (OPENVAS_SCAP_RES_DIR "${OPENVAS_DATA_DIR}/scap")
 set (OPENVAS_SCAP_DATA_DIR "${OPENVAS_STATE_DIR}/scap-data")
+set (OPENVAS_CERT_DIR     "${SYSCONFDIR}/pki/openvas")
 
-set (OPENVAS_SCANNER_CERTIFICATE "${OPENVAS_STATE_DIR}/CA/servercert.pem")
-set (OPENVAS_SCANNER_KEY         "${OPENVAS_STATE_DIR}/private/CA/serverkey.pem")
-set (OPENVAS_CLIENT_CERTIFICATE  "${OPENVAS_STATE_DIR}/CA/clientcert.pem")
-set (OPENVAS_CLIENT_KEY          "${OPENVAS_STATE_DIR}/private/CA/clientkey.pem")
-set (OPENVAS_CA_CERTIFICATE      "${OPENVAS_STATE_DIR}/CA/cacert.pem")
+set (OPENVAS_SCANNER_CERTIFICATE "${OPENVAS_CERT_DIR}/CA/servercert.pem")
+set (OPENVAS_SCANNER_KEY         "${OPENVAS_CERT_DIR}/private/CA/serverkey.pem")
+set (OPENVAS_CLIENT_CERTIFICATE  "${OPENVAS_CERT_DIR}/CA/clientcert.pem")
+set (OPENVAS_CLIENT_KEY          "${OPENVAS_CERT_DIR}/private/CA/clientkey.pem")
+set (OPENVAS_CA_CERTIFICATE      "${OPENVAS_CERT_DIR}/CA/cacert.pem")
 
 set (OPENVAS_USERS_DIR           "${OPENVAS_STATE_DIR}/users/")
 set (OPENVAS_NVT_DIR             "${OPENVAS_STATE_DIR}/plugins/")