That is a tough question. What I did is run mine with the 2 axis controller until I got used to it, and CNC in general. I started knowing nothing about CNC, but have a lot of experience in motion control systems. In the meantime I ordered in all the parts to build a new controller. When the Anilam controller finally failed, I did the upgrade.......right in the middle of a production run. I was up and running again in a day and a half. Finished that job, then started working on the Z axis parts.
I'd agree with Jim, run it as 2 axis till you get it down pat, then upgrade. You can program it from the console, or from your desk top and transfer via a floppy( if you can find floppies anymore) You can also transfer programs via a RS 232 cable, but I haven't figured that out yet. I have the off line software for my desktop, but....you don't really need it, as you can write the program in notepad. It's all text. If it's like mine, there is a DFX converter in the OS. It will also convert G code to a point.
Do you still have the old controller? I found HH Roberts and they have a link explaining that 3200 vs 3300 is one I/O card. I looked and sure enough my board has three slots, and cards only in two. Could it really be as easy as adding another card and updating the software and adding Anilam Z servo set up?