The GPU debug window is absolutely one of the best tools pSX has to offer (even if it is extremely buggy). It let's you find things in record time. Here is a walk-through of how to make the most out of it.
1. Fire up Vagrant Story in pSX
2. Get a roulette wheel on screen
3. Open a debug window
4. Open a GPU window
6. Step through the drawing process until it starts drawing the Roulette
7. This image is interesting, take note of the Program Counter (PC)
8. Place a break point
9. Now open the call stack and inspect
10. This one looks promising
11. Get rid of that conditional branch and test (debug -> run)
12. Okay found it, now let's open a Hex Editor and search for that instruction sequence
13. Apply the patch and save
Now that you know the basic process you can do similar things in future. You don't really need to understand everything that you see. Think of the branches as a sort of flow chart diagram, and blocks of code are only stitched together by the branches.