Edit "/root/ispconfig/isp/conf/procmailrc.master" and add the below ".custom.rc" line.
{MAILDIR_COMMENT}MAILDIR=$HOME/Maildir/
{MAILDIR_COMMENT}DEFAULT=$MAILDIR
{MAILDIR_COMMENT}ORGMAIL=$MAILDIR
{QUOTA}
INCLUDERC={PMDIR}/.mailsize.rc
{QUOTA_COMMENT}INCLUDERC={PMDIR}/.quota.rc
{ANTIVIRUS_COMMENT}INCLUDERC={PMDIR}/.antivirus.rc
{MAILSCAN_COMMENT}INCLUDERC={PMDIR}/.local-rules.rc
{MAILSCAN_COMMENT}INCLUDERC={PMDIR}/.html-trap.rc
{SPAMASSASSIN_COMMENT}INCLUDERC={PMDIR}/.spamassassin.rc
{AUTORESPONDER_COMMENT}INCLUDERC={PMDIR}/.autoresponder.rc
INCLUDERC={PMDIR}/.custom.rc
Now include any custom rules that you may have to the ".custom.rc" file in the users home directory.