Index homing from encoder shall connect to the inputs stated in manual, but you have not been clear how are you getting the INDEX pulse from servo's encoder, some have encoder signal output A B Z and you can connect this Z to pokeys, some drives have referencing or homing as an internal routine which you activate with input to the drive some have both. In drive parameters you set the limit switch input and to which side does it back off and how many index pulses, after its done it will signal you with an output its referenced which you can read in Mach.
Encoder output from drive is usually 5V, if using internal referencing with output from drive it might work with 5V signals (working like NPN or PNP) or strictly 24V.
My suggestion would be some of the CNC4PC boards you mention, I have not looked deep into their manuals but look for 24V IO if not another nice solution which might be all in one is this
http://www.cncroom.com/interface-cards/pobobI made my own boards and have been happy with them 24Vdc IO and 5V encoder inputs