Yeah, it would be nice if you could edit those settings from a GUI. However, that is not so. It's not as bad as it seems though. Maybe the instructions are just too difficult (it's written by engineers after all...)
In your C:\Program Files\MegaSquirt\car1\mtCfg\custom.ini file
Code:
#else ; Actually only good for DualTable and MSnS-Extra.
table = veTable1Map
allowAutoTune = on
corrector = egoCorrection
xLimits = 1500, 4000
yLimits = 60, 90
zLimits = 10, 200
xRadius = 200
yRadius = 7
initialStartupInterval = 1.0
updateInterval = 1.0
proportionalGain = 0.5
lumpiness = 5
X=rpm range
Y=kpa range
Z=min/max VE entry
For example, mine is setup to tune from 1500 - 5000 rpm, 20 - 100kpa (I don't autotune boost) and min/max VE is 15-200.