You did it with "begin logfile" *clone army* "end logfile"? Then no, it won't. If someone else is using that box you can just move their troops aside a little so you can select yours safely. If you saved it as a game, it won't work. Read the v40k userguide that came with it to see how to do what I said above. And yeah, you'd have to control both sides. There's no ai or real game mechanics in the mod, just playing pieces and dice.
This is the 500 (499, actually) point Tau army I came up with a few days ago, it uses the crisis suits and commander as anti infantry, two broadsides as antitank, and two fire warrior teams as "I had to take this but it has no real point":
Shas'o:
-Cyclic Ion Blaster
-Burst Cannon
-Shield Generator
-HW Multi-tracker
-Stimulant Injector
XV8 Shas'ui x2:
-Twin-linked Flamer x2
-Fusion Blaster x2
XV88 Shas'ui x2:
-Targeting Array x2
2xFire Warrior Team x6
Of course, I don't know how it plays. I just know I intended to use the crisis suits the way I used those jetbikes, jump out from behind impassable terrain, fire, jump back, while the broadsides lay down long range anti-armor, and the fire teams sit in cover by them and keep them as safe as possible, should worst come to worst. Could probably be made into a decent 750 point army, to flesh it out a bit more.