I don't use riffworks but I can maybe help about inputs etc.
It is best to plug your guitar into the instrument input - unless you are playing it through something else like certain stompboxes which are outputting line level signal. I know you aren't getting sound through the instrument input but maybe there is some setup thing needing to be adjusted - so I'll just mention some things to check - forgive me if you have tried these already
Plug the guitar into the instrument input (if a normal electric, into the normal instrument input - if its a guitar with ''active' battery powered pickups then probably plug it into the pad one.
Don't worry about any of the knobs on the ux2 except the output or headphones knobs - depending on how you are listening to it. If you are listening through speakers, then a cable should go from the two analog outs at the back of the ux2 to the input/s of the system you are using (these should be line level - so they might say line input on them). Sometimes people are using speaker systems that don't take line ins and so they put a cable between the phones output of the ux2 to the input of their system (this is ok if the system takes headphone level signals). If you are not sure which type you have, its best to try to find out or just be careful with volumes on the knob on the ux2 so that nothing too big goes out to your system.
Then open up pod farm standalone.
Go to 'File', 'Preferences', 'Hardware', 'and click on 'tone direct settings'. This will bring up the Line 6 Audio-Midi Devices box. You can open this from the Line 6 folder too under the tools folder.
Here you can select the sample rate and bit depth etc.
Forget about those just now and just try pulling the sliding lever at the bottom to the 2nd position (or maybe even 3rd or 4th) from the left. I prefer to have it right to the left as this reduces the delay time between playing and hearing the note, but its best to try it first a bit over to the right as this allows things to be setup and then once everything else seems to be working, then you can move it along until it sounds good and without any pops or hiccups in the sound.
Then press apply (if it is there to press) and ok and go back to pod farm standalone and ok the preferences screen. Its probably best to close pod farm and restart it and then go to 'mixer' view. In here, make sure that the first input says 'instrument' and that the other input is not active. In Tone A, turn the 'D.I. Level' right to the left as this controls how much bare guitar sound you get. Then select an amp etc. to use or a preset amp setup, and make sure the amp has some drive and some output volume.
Then try playing and check that there is signal in the top left input 'in' meter and that there is some ouput on the top right meter. If not, turn up the out knob.
As I said, you might have done all of this but I thought I'd try some things first and see if anything helps. If its still not working, let me know and I'll try to help further.