I know we need to be to the Lima airport about 3 hours early for our flight returning to the states, but how about a morning flight from Lima to Puerto Maldonado? Is an hour enough time or should we leave 2? We will be traveling in about a week and a half, if that makes any difference. Thanks!

One hour will be fine if you have your boarding passes. If you are flying Lan you can print them out 48 hours prior to your flight.

Be sure to confirm your flight time that morning. Lima airport takes about an hour to reach from Miraflores. One hour should be okay if you have a boarding pass, the airport is fairly small. You will need to pay your departure tax and sometimes that line can be long, I might allow a bit more than an hour to be safe.

We can print out our boarding passes before we leave the states, but since we will still have to check luggage, does that make a difference?

Near the counters there is a "bag drop" for people with boarding passes, there will probably still be a short line for it but you won't have to check in at the counter. BTW you will find English speaking LAN agents at the Lima airport, no worries.