Hi karpa
What operating system are you actually running on your PDA? You say you chose "Windows 2003 Device" but this should not be an option as a target PDA device.
Both LabVIEW and the SDK you mention will do essentially the same thing. Both will allow you to compile and run your own programs on your PDA. You would most likely use one or the other, unless you write code in one that you wish to call from the other.
As for your devices, how do they connect to the PDA? Running LabVIEW code on your PDA will allow you to interface with instruments via serial ports, etc.. If you create a VI under the PDA target in the Project Explorer (which you say you have done) you will be able to see all available functions on the Functions Palette for the Block Diagram. Check these to see if the communication method your other devices use are available.
Hope this helps!
Brian A.
National Instruments
Applications Engineer