I just send MIDI from my DAW to the synth I want to sequence, then go from the audio outs of the synth to the audio inputs of my soundcard, record enable a track to monitor what I am doing, build the patch exactly as I want to and when ready, press record and thats it.
Mono synths cover the mono sounds. Then depending on what stereo image I have available (and what is going on in that particular part of the track) I might just record the synth in mono and leave it in the centre (if there are other stereo sounds layered at that part). I might record the synth through the Moog MF-103 and bi-phase that give a nice liquid and moving stereo image, or I might record through the Moog MF-108 that has the wet effect, out of phase on one output and have a stereo image that feels further wider than where the monitors are placed....or I might just double track the mono synth and pan left/right the two channels. Playing with the stereo image like this give a wide track and helps with mixdowns as if you have to have sounds that are clashing in frequency and timing, you can put them in a different position in the stereo image to achieve definition. Also using different reverbs and put them in different "rooms" helps the brain identify them easier.