Strangely enough, I just set up a 8GB CF Card on my A4000 using PFS3 v5.3 and as Thomas said, I used PFS3DS.
Just in case you hadn't seen it, when you use Hard Drive Toolbox to partition the CF card, use the "add/update" button and then select "Add New File System". Out of the choices thrown at you, you'll see "PFS3" and "PFS3DS", select the "PFS3DS" option and (in my case) is was loaded as Custom File System "CFS\00". Use that when you click the "change" button to select the file system to use with the partition.
I just set up a single 8GB partition and it is working fine. All other options for HDToolbox were set automatically by the software with no fiddling required.