There isn't really a best practice, but there are several options. In this case, as I understand it, you will need to set them up as separate MIDI/Synth and Audio tracks - not as Instrument tracks.
The idea is that you will have 1 MIDI track and 1 audio track for each instrument in Play. Each MIDI track going through the same instance of Play needs a different Channel number. Those channels need to be set to correspond to the right instrument within Play itself.
Then, those instruments in Play each need to be set to the various outputs: usually the first one goes to "1/2", the second goes to "3/4", etc. These are stereo pairs.
Finally, your audio tracks 'pull' the audio from Play by assigning their input to the appropriate Play output. So set one to "Play 1/2", the next to "Play 3/4", etc.
It's probably best to start off simple to make sure you can get it right: add 1 instance of Play to the Synth rack, load up 2 instruments in there, make sure their channels and outputs are set differently. Now add 2 MIDI tracks, route them to Play and the appropriate channel. Add 2 audio tracks, make sure they're listening to the appropriate Play outputs. If that went well and each MIDI track is playing different instruments, add extra tracks and instruments to taste.
How many instruments you have in each instance of Play is up to you. I like to run 6 instances, each with 4 to 8 instruments loaded: strings, brass, wind, pitched percussion, unpitched percussion, and choirs.