I can make the various Index moves from the Drive Support Tool software but when I try to do it from the PLC I/O it will only do Index0 or won't do any of them at all.
This will generally be caused by using the incorrect Action setting in your Indexer Parameter settings. If you want control to be via inputs defined as ISELx inputs then the Action should be set to "Wait for Start" for each of the Indexes. With this Action the indexer will look at the ISEL input pattern when the defined Start input is activated (rising edge).
If the Action is set to "Stop" then the indexer will look at object 0x3008 to determine which index to run when the Start input is activated (rising edge). The default value for 0x3008 is 0 (Index0). However, if 0x3008 is set to a value of 64 then it will force it to look at the ISELx inputs and will thus act similar to the "Wait for Start" action. See picture below in reference to changing the value for object 0x3008.
Mixing "Wait for Start" and "Next Index" may be useful for some external input control combined with some automated indexing sequences. Also, mixing "Stop" and "Next Index" may be useful for the same reasons. However, mixing "Stop" and "Wait for Start" Actions may not provide your desired sequencing.
Another item or two that may prevent the indexes from running (both from external control and via the Drive Support Tool) is the 'Control Mode' not being set to Indexer (Index is the default setting for object 0x3000) or your Input definitions for the ISELx inputs not matching your actual physical wiring.