The best way would be to remove the harddrive from your Amiga, connect it to the PC and use WinUAE to make an image file. This would include the partition table and all partitions, so that you have a true image of the whole HDD. There is a button in the Add Harddrive window to do this.
With AExplorer you can only transfer single partitions. If you open Amiga Explorer on Windows, you'll see System.HDF and Work.HDF in the list. Just drag them to a folder on the PC.
With a little more effort you can make a harddrive image with both partitions in WinUAE. On your Amiga run a tool which can save the partition table into a file, for example
TSGUI. In TSGUI select a partition of your HDD, then choose "save RDB to file" from the menu.
Use AExplorer to transfer this file to the PC, too.
In WinUAE create a HDF which is at least as big as your real HDD and click on "Full drive / RDB mode".
Boot from another HDF or a folder which contains TSGUI. Also add the folder with the two HDFs to WinUAE.
In WinUAE run TSGUI. First choose "restore RDB from file" from the menu, select the RDB file and your big HDF, save the RDB and reboot. Run TSGUI again, you should now see the partitions in the list. Select one partition and the corresponding HDF file and click on "File -> Disk". Repeat the same for the other partition.
Remove all other drives from WinUAE except the big new HDF. Reboot and you should see your Amiga's OS.