GGiorgakis,
Capsule Connect VPN is a full VPN client. You have to configure remote access rules to use them.
These rules are different from MobileAccessBlade rules, they are the same as for a normal Windows VPN client like EndPoint VPN.
If you use SSL-extender and native applications via MOB, you can't use this rules with Capsule VPN.
Add your gateway to the remote access community, create rules with users as source, your needed destinations and services and in the VPN section add the remote access community.
Wolfgang