OmniRig is a CAT software from dxatlas.com and its config program is sort of a small box on the screen, much higher than wide. OmniRig itself will be called in the background when you have configured CAT in e.g WSJT-X, JS8Call or HDSDR ("Omnirig Rig 1"). You will be mostly fine if you use the OmniRig FT-991 ini files fresh downloaded from dxatlas.com, otherwise use mine FT-991-SA7CND.ini on http://sa7cnd.se/ somewhat updated by me. Put it in the folder C:\Users\yourusername\AppData\Roaming\Afreet\Products\OmniRig\
FLDIGI can not use OmniRig, so a COM port Splitter such as VSPE is needed for FLDIGI cooperation with "omnirig programs", and then you can config FLDIGI with e.g RigCAT and a FT-991 xml config file. Mine FT-991-v2.xml is enchanced, on my radio page. Put it where you can find it and link to it from FLDIGI Config - Rig Control - RigCAT.
It can be a good idea to study the FT-991 CAT Operation Reference Manual also.
With the VSPE Com port Splitter I now mention on my radio page, I can run several of the programs I mentioned above at the same time, so you could also - with some work and trials perhaps...Hope this helps, GL.