Hi Robert,
I don't have a FT-991a but in general:
1. Go to Tools->Audio Config. The radio's sound card is typically chosen for "Input To Computer From Radio" (Receive tab) and "Output From Computer To Radio" (Transmit tab).
2. Next, go to Tools->PTT Config. You can check "Use Hamlib PTT" and select "Yaesu FT-991" from the "Rig Model" drop down menu. The serial device is the same as what is configured for other applications for CAT control (e.g. WSJT-X).
and optionally (but recommended):
3. Go to Tools->Options:
a) In the "Reporting" tab, check "Enable Reporting" and enter your callsign and grid square.
b) In the "Modem" tab, check "Simultaneously Decode All HF Modes".
Hopefully that helps. Let me know if you have any other questions.
Thanks,
-Mooneer K6AQ