I would like to run XM in pulse mode: I want to run 1MHz where I want pulse width of 200ms and pulse rate of 1Hz. Can it be done, if so, how?

You can do it manually (without any external electronics) :

Go to the main menu of the XM generator:

Then CH1 (F2) - Down (F5) -Down (F5) - Burs (F4) - Select "TrigMode" = "CH2_Out"

What you do is this:

Select CH1 the 1 MHz, then use CH2 to Trigger the BurstMode of CH1 (the output of CH2 is internally connected to CH1, you do not have to connect it by yourself) 

So Select manually:

CH1 = 1 MHz
Go to the BustMode of CH1 (See above). Then select:
N = 200000 (= 200000 Cycles every 1 Hz = 200 ms Burst)
To Start press "Run" in the BurstMode Menu of CH1

CH2 = 1 Hz, Square wave

If you do it correct, then you get this (on CH1) :

You can do it also over the Spooky2 Software (with one Restriction) * :

Select for OUT1 : 

Square Wave

1 Hz / Duty Cycle : 20 % 

* (The value of the Duty Cycle for OUT2 can not setup independently so it has to be also 20 %)

Select for OUT2 : 

Square Wave

F 2 = F 1 x 1000000

And use the Option: Modulate F2 using F1 (AM DSB)

For more details, please check this link:
https://www.spooky2.com/forums/viewtopic.php?f=12&t=7925