Rafa,
I'll preface this that I've only used CANOpen on one project, but it was with encoders and was fairly involved.
Getting the data out will likely not require any concern with sub-indices per se. Identify the address that your process data is getting transmitted with, and use that with the CAN Receive function block. The data, which is spread out in multiple bytes, can be combined using the 'Combine' function block in the 'Data Conversion' section.
Sub-indices are entered into your CAN message structure as part of one of the data bytes. Somewhere in the encoder documentation it probably shows message structure something like this image:
Also in your encoder documentation should be a list of Commands, Indexes, and Sub-indexes
Using that structure you just fill in the ID and the data bytes as shown. The COB-ID is going to be maybe 180h+node# or 280h+ or 380h+ depending on if you're interested in PDO1, PDO2, or PDO3. The Command will depend on if you're sending data to the encoder or telling the encoder to send you data, and it may also vary depending on the length of the data. Index is basically the parameter that you're interested in, and the sub-index identifies what aspect of that parameter you're interested in. For example, sub-index 2h for PDO1 (Index 1800h) may control whether or not PDO1 sends data synchronously or asynchronously while sub-index 3h of that same 1800h Index may control an inhibit time on the PDO1 data transfer. As shown in the above message structure, the Index and Sub-index go into what you might typically use as your data bytes. Finally, at the end of that structure is the Service Data which for in something like commanding inhibit time on PDO1 you would put in those bytes the desired inhibit time.
Look through your encoder CANOpen manual to correlate this stuff. Log into your CAN sniffer and see what works. Doing stuff like commanding an inhibit time or synchronous data transfer requires a sequence of commands to put the encoder into a certain state and then save and reset the encoder when you're done.
Thanks,