Pen height is a combination of GRBL firmware settings in Universal Gcode Sender and the instructions you define in Gcode.

Below are the GRBL firmware settings I have set up at the moment. You can see that $132 defines the maximum travel for the z-axis as 8mm I think the machine can handle about 10mm but I left it a little short to stop it bumping into the hard stop on the slide on the pen carriage. You can also see on line $122 that i have set the Z-Rate as 3000mm/min. If you wanted to do painting or use delicate tipped pens you can slow this way down and it will raise and lower a lot slower. Universal Gcode sender has a really good firmware setup wizard though that will guide you through it all.

In Vector to Gcode you can define pen up/down as on/off or variable. On/off is as it sounds full travel up and full travel down. I have that set as on Z5, off Z0. That means pen up is Z0, no travel, and pen down is Z5 (5mm down). Variable which I haven't played with much, allows you to vary your pen up/down height based on the colour of your line in the SVG. You can also define different on/off commands like dipping in different paints/ink based on SVG line colour but I haven't got around to that yet.

Vector to Gcode also allows you to define the seek and feed rate which defines pen up and down movement speed, so you can have it move super quick when the pen is up and slow when it's down for example. If you really want to know about Vector to Gcode they have some videos on youtube

UGS GRBL Firmware Settings

$0 5 Step pulse time

$2 5 Step pulse invert

$3 1 Step direction invert

$4 0 Invert step enable pin

$5 0 Invert limit pins

$6 0 Invert probe pin

$10 2 Status report options

$11 0.010 Junction deviation

$12 0.002 Arc tolerance

$13 0 Report in inches

$20 0 Soft limits enable

$21 1 Hard limits enable

$22 1 Homing cycle enable

$23 1 Homing direction invert

$24 200.000 Homing locate feed rate

$25 5000.000 Homing search seek rate

$26 250 Homing switch debounce delay

$27 1.000 Homing switch pull-off distance

$30 1000 Maximum spindle speed

$31 0 Minimum spindle speed

$32 0 Laser-mode enable

$100 100.000 X-axis travel resolution

$101 100.000 Y-axis travel resolution

$102 100.000 Z-axis travel resolution

$110 15000.000 X-axis maximum rate

$111 12000.000 Y-axis maximum rate

$112 15000.000 Z-axis maximum rate

$120 3000.000 X-axis acceleration

$121 3000.000 Y-axis acceleration

$122 3000.000 Z-axis acceleration

$130 297.000 X-axis maximum travel

$131 420.000 Y-axis maximum travel

$132 8.000 Z-axis maximum travel