OnCommand System Manager 3.1.2 is a java application+flash UI installed on your workstation, and then launched, accessed by HTTP to localhost, and then the application is pointed at the IP addresses of your NetApp systems.
In some cases, administrators and implementation staff may create a VM and install it on that, but it is not required to do so, so it may not be present.
That is 2 questions in one although they might be connected.
Both, System Manager and NMC are client programs you can install somewhere. System Manager connects to Ontap as Alex described.
NMC connects to Unified Manager Server to Manage Backups in ONTAP.
Both problems could be caused by settings in ONTAP or Network or settings on the client. The documentation says which ports are in use. In the ideal case you would make sure that all the preferences in the documentation are met.
If this is the case opening a support case is probably the easiest way of solving it.