To change the Font or Colors that SciTE use when editing an AutoIt3 script press Ctrl+1 within SciTE, the below screen will popup.
Change anything you like and press the Update button to save all changes to SciteUser.Properties.
To revert back to the last saved changes click Reset.
To remove all your changes and goback to the defaults click on Remove.
The program will ask to restart SciTE to activate your changes.

When you do "User Option File" to open your SciteUser.properties file, it will contain something like this:
#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#
Created by SciTEConfig
#------------------------------------------------------------
font.base=font:Verdana,size:10,$(font.override)
font.monospace=font:Courier New,size:10
font.override=$(font.monospace)
use.tabs=1
indent.size=4
tabsize=4
indent.size.*.au3=4
#Background
style.au3.32=style.*.32=$(font.base)
#CaretLineBackground
caret.line.back=#FFFED8
#White space
style.au3.0=fore:#000000
#Comment line
style.au3.1=fore:#009933,italics
#Comment block
style.au3.2=fore:#669900,italics
#Number
style.au3.3=fore:#AC00A9,italics,bold
#Function
style.au3.4=fore:#000090,italics,bold
#Keyword
style.au3.5=fore:#0000FF,bold
#Macro
style.au3.6=fore:#FF33FF,bold
#String
style.au3.7=fore:#9999CC,bold
#Operator
style.au3.8=fore:#FF0000,bold
#Variable
style.au3.9=fore:#AA0000,bold
#Sent keys
style.au3.10=fore:#FF8800,bold
#Pre-Processor
style.au3.11=fore:#F000FF,italics
#Special
style.au3.12=fore:#A00FF0,italics
#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#