Here is what i do in Pro Tools:
1. Load up Spark on an instrument track
2. When Spark is loaded up in Pro Tools, i go to the automation-page thatīs specific for Pro Tools.
3. I choose the LPF cut and LPF res from the automation-page (This will automate ANY of the filters on the FX-pad)
4. I Press record on the Spark instrument track, and record the automation on the instrument track.
5. Now i choose a new Audio track, and bus Spark instrument track over to the audio track and record the automation that way.
Itīs a pain, it really lags, and i really do hope they integrate FX-pad automation IN SPARK eventually
Since itīs such a pain, what i typically do is experiment with the FX-pad, and when itīs time to really import stuff in Pro Tools i use my own filters, gates etc.