I have had the pleasure of using all the above tuning software, and hands down neptune is by far at the top of my choice for Honda ECU tuning, It is very stable, responds when you need it to, updated on the regular, and supports just about every option the S300 does without the need for a internal hardware unit, unless you want to run the Neptune RTP which does the same as the tuner version but also does on-board datalogging the same way the S300 does. I have never been able to create a basemap for a customer faster then I can with neptune. set the initial perameters, set the injector size and bam, 98% of the time the car runs better then most new basemaps out there.. I for one dont care for Hondata's customer service, but thats just me.

To anwser your dual maps question, any system like Neptune and the S300 allow you to run dual maps many different ways such as

On a switch(toggle switch)
RPM activation
Load activation
TPS activation

Set the minimum and maximum points and when they are met your ECU will switch maps.

So if you wanted to switch to say a diff map with TPS, all you would do is set the TPS setting to say 90% and any time you reach that TPS or higher you switch maps, same goes for the other listed activation inputs, other then the switch, which is what most people opt to use.

My biggest thing is to go with whatever system your selected tuner is comfortable working with, as all the above systems will make good reliable power in the right hands.