We have all our trucks GPS'ed, which is a great fail safe for double checking discrepancies. We have a time clock system(can't remember the name off hand) where guys call into a number, and enter the job code for the job they are going to and it clocks them in. Same way to punch out, so if they have to go to another site that day, they call in with that code. Great system, but like anything it has its flaws.
I would get away from paper cards as quick as you can. We did them for a long time, too long probably. I have never regretted spending money on efficiency upgrades.