I can't speak for your machine because I don't know what kind it is, but your first paragraph does not sound right to me. Your second paragraph is the way I use my machine.

I hook up my manifold gauges normally and then hook the center hose to my recovery/recycle machine.

Basically these machines allow the pressure of the system to force the refrigerant still remaining in the system into the recovery tank until it no longer has pressure to cause flow. Then the machine provides a vacuum to draw the remaining refrigerant, mostly for environmental reasons to ensure that there is none left in the system to escape to the atmosphere.

You can open both sides of the manifold while recovering because you must do this with the engine off and the system not running. If you do it all through the low side it will take much longer.

Good luck,