Hi Nick,
Yes but would be helpful if we knew what ArcPad version you are using and what iPAQ device used as there are compatibility concerns between ArcPad and Windows Mobile OS of the iPAQ device. Typically, a user can connect to the GPS from within ArcPad using the Find GPS utility. Once connected and GPS is on and running, open ArcPad and select GPS > GPS Preferences > GPS tab and run Find GPS utility (black binoculars) to search for the connected GPS. Please review the ArcPad Help for more information.
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Cheers,
Denise