Hmm... I'm not sure whether motherboards are specific about VC memory. For sure the ATI R9550 EE is an AGP 8x card with 128mb; 128bit memory. This card has very good reviews both in the gaming and vc overclocking scene. The nVidia GeForce FX5200 is also an AGP 8x card. If you compare these two, the R9550 far outperforms the FX5200 since the R9550 is a mid-end card and thus is segmented to another price segment.
You won't have a problem with the AGP issue however because it is backwards compatible. The catch is that you just can't use the full potential of the card. It's not that bad after all. You're still better off when you upgrade to another mobo in the near future. I recommend that you try those two cards and whichever goes well with your mobo, choose it and return the other. Just make a deal with the salesperson to let you have a taste of those 2 VC's before deciding to buy.
Also check if your
POWER is sufficient for those VC's. The FX5200 consumes about 65 WATTS of power from your Power Supply Unit (PSU) and the ATI Radeon 9550EE consumes about 45 WATTS. You add that (the AGP VC) to your other components such as the CPU, hard disks, optical drives, usb ports, etc., and a 300-WATT PSU might be insufficient.
As my final thought, try out those 2 VC's first (if you can) before you buy. If your budget is within these price ranges (FX5200 & R9550), I strongly suggest you try out the R9550 first, it's fast and consumes much less power than it's nVidia counterparts. Download the latest catalyst drivers for ATI. There are many Radeon drivers out there, but try out the official release from the ATI website first before exploring those optimized drivers.
You can have your system specs posted here so we can verify if your proposed VC's are compatible. You can easily do this if you have NBA Live 2004 or 2005. EA Sports has this Info tool that displays your system info summary.
Reference
Power Supply Wattage Calculator