Check the "Config" section of the JD-990 editor to make sure that the setting for Device ID match what's set on your synth.
Patch Base cannot automatically determine which if any PCM card you have installed in your JD-990. If you have a PCM card installed, open the "Config" section of the editor and select the card you have installed. This will ensure that the correct options are shown to you in the Patch and Rhythm editors when selecting Waves from Card.
The Voice editor gives you two modes of designing a voice. The tabs A–D let you see an entire Tone on a single screen, to edit any parameter for that tone. The Pitch, Filter, Amp, LFO, and Ctrl tabs give you a "Palette" editing mode, where you can view and edit the parameters across all 4 Tones for a particular section of the voice.
Depending on your MIDI interface, your JD-990 might show an error when sending a full Rhythm kit from Patch Base. If this happens, lower the Transmit Speed for your MIDI Interface in Patch Base's MIDI Settings / Preferences.
You can fetch and edit each of the 7 voice parts in Performance mode from Patch Base. But, JD-990 units running firmware before version 1.03 have a bug that prevents fetching these patches correctly. Older units can still receive patches and parameter changes though.