I have an NVidia FX 5500 PCI 128 MB Video card that when I run Sax2 -p to probe for it, it shows this:

Chip: 0 is -> Intel i845 00:02:0 0x8086 0x2562 PCI i810
Chip: 1 is -> NVidia GeForce FX 5500 01:10:0 0x10de 0x0326 AGP nv

Oddly enough, my NVidia card is PCI and not AGP. I have 2 questions: How can I remove the Intel from being read by Sax2 and how can I change my NVidia card so that it is read as a PCI card instead of AGP?

Without wanting to be rude, as long as the card works who cares what it is detected as?

I tend to agree with acidzebra.

Having said that you might be able to disable your vga function on the Intel chip by using the motherboard's BIOS CMOS setup.

You can get a better idea of what Linux sees by using the hwinfo utility. The hwinfo utility creates thousands of lines of output so the output of this utility should be put into a text file and then read via less.

hwinfo > hwinfo.txt
less hwinfo.txt

You can also use lspci to see a briefer report. This utility will only output a few lines so you can use it on a terminal window and then scroll back to read the beginning of the report.

Nevertheless I'll end as I started by agreeing with acidzebra. In general on a production system if it works then don't fix it.

If you are experimenting on a test system or on your own personal equipment in order to learn more about the system then that's always a good thing. Since you are asking about a high performance graphic card then I would guess that this is your own personal equipment.