Create a New Physical Inventory. There is an "Import" button on the properties page. This can be used to import a CSV text file - the file should have either 2 or 3 columns : ItemLookupCode, count and optionally CountDate. The import button will start a simple wizard that will help you import your inventory data. The help file is pretty good - if you have specific questions about using Physical Inventory import, post back...
You can also import into some Inventory Wizard tasks, but the file formatting is a little more complicated - you have to match the columns displayed in the wizard and each wizard is different...
I have never used the M5000, but every data terminal I've seen ends up creating a CSV file, so the physical inventory toll should work fine.