I've moved this thread to RGSSx Script Support. Please be sure to post your threads in the correct forum next time. Thank you.
I imagine the position on screen is determined by the position in the Troops tab.
AS far as your other issue - please provide a link to the script so people can see how it's set up. Apart from you being mixed up about the number of rows and columns (it has 13 rows and 4 columns, not 4 rows and 3 columns), it LOOKS like you've set it up correctly within the script (or note box).
The character isn't a troop, It's a character and it's not in the troops tab to adjust sadly.
You need to adjust the characters in the actors battlers script from what I found
VE_POSITION_ADJUST = {x: 0, y: 0}
#--------------------------------------------------------------------------
# * Actors battlers position adjust
# Used to adjust the position of all actors battlers.
These are the positions for a 4 party group however my game will only use one hero so he would be only actor 1
VE_CUSTOM_POSITION = {
# Position
1 => {x: 420, y: 182}, # Position for the first actor.
2 => {x: 424, y: 218}, # Position for the second actor.
3 => {x: 428, y: 254}, # Position for the thrid actor.
4 => {x: 432, y: 290}, # Position for the fourth actor.
} # Don't remove
And when I edit the Y coordinate it doesn't change the position at all.
Also edited in a link to victors google drive with all his scripts.