Here's a quick and dirty step by step guide:
disconnect peripherals such as rudder pedals and sticks before opening TS3 (if you have had problems setting push to talk keys).
open TS3 and connect to a server then go to Settings>Setup Wizard> and set your main PTT key.
to set up a whisper to another channel, for example BAP1, go to Tools>Whisper Lists> and a window opens - on the bottom-left press the 'new' button and a grey dialogue box opens asking you to select the key you want to use as your PTT whisper key. Choose the key you want to use to whisper to BAP1
You have selected the key you want to use for this whisper, and at the centre-top of the window there are two boxes - 'Hotkey' which shows the key you have selected, and 'Whisper To' which should show 'Clients & Channels'.
On the right of the window should be a list of the servers you have in your server list - click on the GIAP server and you get a list of all Clients and Channels within the GIAP server.
To assign your selected key to whisper to the BAP1 channel, click on Channels, then find BAP1 and drag'n'drop it into the centre of the window.
Hit Apply then OK.
Next go to Settings>Options>Whisper> and you need to uncheck the box 'Always show whisper history when receiving a whisper'.
Hit Apply then OK.
This is important, otherwise every time you get a whisper a dialogue box will appear telling you that you got a whisper which will probably dump you to desktop each time!
And that's it!
Rinse and repeat for all other whispers.
To set up Channel Commander
whispers, right click on your name in the main TS3 window and toggle Channel Commander, and then go through the whisper setup as above EXCEPT you need to set the 'Whisper To' button at the centre-top of the whispers window to 'Groups' by clicking on it and selecting it.
I'm sure you can figure it all out from there!!