OK. You will have to change the sprite placement information for the character you are switching.
The placement information for the 2nd Kain (the sprite I changed in my hack) is at 0995D0. Whe you go to that location, you see this:
0F 04 05 C2
0F = ID for Kain sprite
04 = X value on map
05 = Y value on map
C2 = direction, palette, speed, etc.
I wanted this sprite to be Golbez, who appears in the entrance to the Sealed Cave. So, I changed the values to:
13 04 0B 54
(Normally you would use 24 for Golbez rather than 13, but I switched Edge and Golbez in my hack.)
I think you said that you used the Paladin Cecil slot for your playable Anna's sprite. Now, I haven't tested this yet, but try changing the values to something like this:
C3 04 03 54
C3 = ID for Paladin Cecil sprite
04 = standing in front of the door on the X-axis
03 = standing in front of the door on the Y-axis (I think)
54 =normal walking speed, facing up toward the door, not walking in place
You don't have to worry about palettes when placing player characters, because the player character palettes override whatever townsperson palette would otherwise be displayed. But, you might have to try different values for that fourth bit to get the direction and movement speed that you want.
I don't have very good comprehension of how that bit works, quite frankly, so I just experiment with it.
When messing with non-player sprites, just play with the value of that fourth bit to switch the palette. Bumping it up by 10 seems to cycle through the palettes. Each time you loop through the palettes, the movement speed increases. Changing the value by 1's instead of 10's will cycle through all the directions the sprite can face. Just play with it a bit and you'll see what I mean.
So if you want to change the palette of Rydia's mother, you would just have to find her sprite in the placement data and alter it. I don't think you can apply Rydia's palette to her, though... I think it only loops through the three townsperson palettes plus the Black Chocobo's palette, but frankly, I haven't experimented enough to know for sure. The ID for Rydia's mother's sprite is 5A, woman lying down. I think there are only two instances--Mist and Toroia.