no, it's not a bad idea. your card will like you for it
anyway, when measuring the resistance (in ohms) you don't need the PC on with the card in. in fact it's better if it isn't on when you're measuring the resistance.
but if you wanted to measure voltage, you'd have to have it on.
and yes, that circuitwriter pen is the right thing to use.
anyway, to the above post:
increasing voltage increases heat output. since P = VI (power in Watts (watts = joules per second) is Volts x Amps)
heat is energy converted from the power you put into the card. it can also be measured in Watts (joules per second)
the more watts the card recieves, the more watts of energy it outputs as heat.