Firstly if the battery is suspected of being flat, indeed marginal for a start, then there is one switch you would not operate.
(trimmed)
Now this is where you need to know your aircraft... the one switch I would not be touching is the starter !
That can make life very difficult, indeed possibly a show stopper.
(trimmed)
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Once the starter has been operated a failed start will mean the Bendix will remain engaged.
Agreed, but you forgot the other problem associated with marginal batteries <reffered to as MB from here on in.
How many pilots/car drivers have you seen attempting an MB start where it struggles through the compression, or even worse tapping the starter button until it finally gives up and goes through the compression? I bet not one of these people realise just how much damage they are doing to the starters internals, and potentially to the battery itself.
LAME's bank accounts love these dopes.
Many Pilots have no idea how to swing start an engine safely
I'll cheerfully put myself in this category. Aware of the dangers, aware of the cockpit drill (for 2 person swinging). Something I might go and learn sometime.
So on certain aircraft and you think you may have a marginal battery the best thing to do would be to break out the cellphone and ring the LAME. Leave ALL switches in the aircraft off..
Don't even hit the starter, Alternator switched off or not.
Or if you have the equipment, and knowledge, then go GPU and end the MB situation.
Now back to the question about where to have the switches during a normal start..
I would be reading the POH and listening just a little to the instructor. If there is any difference then it would be time to quiz the instructor a little more about it.
I prefer to ask questions like these of several instructors as a group,

then kick back with a beer to enjoy the fireworks. Then check what I learned with a LAME.
We had a conversation about this very thread at the aeroclub on sunday, and I thought now was an oppurtune time to recheck my thoughts....so opened my travel-air manual to x-check my recollections of the procedures and why.
The Be95, has 2 big arse ALT FAIL lamps set high on the coaming. In the pre-start, you use the Test button to make sure they light up. To keep it simple...
.....Master on.
Alt on
Alt warning lamp should illuminate.
Light the fire
Alt lamp should extinguish
Check amp metre, once it falls to its lowest point, light 2nd fire.
Doing it this way shows that the failure warning circuit is working as advertised.
If you start it with the alternator off, the fail lamp will never show you if the warning system is working.
Enjoy!
Cheers little ears!
Jas