Currently, it is not possible to configure the DNS suffix (search domain) for SSL VPN and IPSEC tunnels through the GUI, but it can be configured using the CLI.
config vpn ssl settings set dns-suffix example.com example.org end
config vpn ipsec phase1-interface set domain example.com end
Changes are effective immediately. After configuring the setting, users will be able to resolve names using single names instead of FQDN.
A note of caution: when installing the Fortinet SSO Agent on a server, the option to secure connections from a FortiGate with a password is enabled by default, and a random password is assigned.
You have to turn off or change the password before you add the SSO agent in your Fortigate.
There's no mention of this in the manuals, so now you know...