Hello Scott
The computer software arranger will never be as easy to operate as a hardware arranger keyboard or organ. (Exceptions are the Wersi OAS instruments and the Lionstracs Mediastation, (Although the Mediastation does take a bit more knowledge as you have to set up jacks for input and output of the VST, were as the Wersi OAS system does it for you automatically) which have the computer and keyboard contained in one unit)
The best way to think of the set up is like this: your controller keyboard is the same as the keyboard on your arranger keyboard, the arranger software (OMB etc) is the same as the controls on an arranger keyboard, and the software VSTs are the sound engine of the arranger keyboard or Midi expander module.
Here is a good way to get started.
1. When first starting with software, I would suggest setting your controller keyboard to output on channel 1, and OMB etc to receive on channel 1, leave the rest of the settings on default (Internal computer sounds) and then play around with the software as you would any hardware arranger keyboard. (This will allow you to get you used to its operation and quirks)
2a. Set up your VST instrument to run on its own, (Do not run OMB etc) and set it up to receive on channel 1, then get used to the feel and operation of the VST by playing it directly with your controller keyboard.
2b. Split your controller keyboard, leaving the right hand side to send on channel 1 and the left hand side to send on channel 2, and then get used to switching between channel 1 and channel 2 in the VST, including changing the sounds for each channel. (This will allow you to get used to the operation and quirks of the VST)
3. When you have gained experience using the programs separately, you can then run OMB etc, and the VST together, and set them up to communicate using the internal Midi channels. (Because you are now used to assigning channels separately in the programs you will find that you will be able to set them both up fairly easily)
Hope this helps.

Bill