Yes, removing the evaporator assembly is an incredible pain in the butt. I've had mine in and out several times after I retrofitted a/c into the car at least 15 years ago, and each time, I think that plastic piece that mates the top of the evaporator to the rest of the air flow system is going to shatter into a million pieces.
You say "When I took it out and disconnect the two pipes leading into it nothing came out of the pipes. I had thought whatever amount of R12 I had put in would escape then but there was nothing." Just so we're all on the right side of the law and we all have a clean environmental conscience, what you really should've done was a) hooked up a gauge set to the car with everything off and seen if you had any resting pressure in the system, indicating the presence of gas (R12), and if you did, b) taken it to an a/c shop for them to recover it. But, yes, if you disconnect the pipes (or depress the charging valves) and nothing comes out, there's nothing in there.
You say "However, the compressor clutch does not engage. Is this because the system is empty or did I screw up the compressor by turning it on for a short time while on 'empty'?" Most systems are installed with a low-pressure cut-off switch that prevents the compressor from engaging if the system is empty. When recharging, you either need to recharge slowly so R12 wafts into the system until there's enough pressure for the low pressure cut-off switch to see, or bypass the cut-off switch.
But... before you do anything, since you've had your system apart, I strongly recommend you leak-test it. The single longest chapter in my book is on air conditioning, but basically you need a gauge set, a tank of nitrogen, and adapters to hook them together. You first pump the system with 50 psi of nitrogen and listen for big leaks. If you don't hear then and if the gauges sit at 50 psi, then pump it up to, oh, 100 to 150 psi. Best to let it sit overnight. If it's still at 150 psi in the morning (may be slightly lower if the garage cools at night), then you're good, but if it's down, you've got a leak and you need to find out where it is. If it's in the evaporator you've just installed, you get drunk, cry, and get drunk some more (been there done that).
You really need to do this before you recharge with R12. Once it is leak-free, you evacuate it (pull a deep vacuum for at least 45 minutes to boil off any moisture), then recharge.
Or take it somewhere and pay them to do it. No shame in that. I did it for years (replaced parts but paid someone else to leak-test and evacuate) before I began doing it myself.
--Rob