Probably not every substructure you want is included in the MOLGEN package. So you might need to create new substructures based on available ones or based on a generator result. This can be done with the aid of MOLED.
MOLED can of course be started just like any other executable. Every single substructure is saved in one file. So you can load and edit existing substructures easily. Apart from this, several entry-points exist inside of MOLGEN from where you can start MOLED. Having started MOLED, the following window will appear. If you start MOLED from MOLGEN, a certain structure might already be loaded.
In MOLED there exist different editing states like inserting atoms, inserting substructures, inserting bonds ... . These editing states correspond to certain buttons in the MOLED window. The actual editing button is marked with a red frame.
There are the following command-line options for MOLED:
moled.exe