Where will I clear security coming back from Europe?

Nowadays you don't have to go through security again in Amsterdam but you will have to go through passport control. 1 hour? Depends how long will be the line and also if your plane is just little bit delayed it's pulling devil on his tail. I would go for two hours to have peace in my mind.

You need to clear security for each and every flight. But, that is the wrong question. The question is how far in advance do you need to check in for your flight from Rome? Your airline should tell you this, but 1 hour in advance is typical.
I am assuming you are doing this as one booking with one ticket. In this case you would not have been sold the ticket unless there was enough time for the transfer. 1 hour is just enough time at Amsterdam; but, if your first flight is delayed, it is the airlines responsibility to put you on the next flight.
The next question is emigration and customs. If you have a through ticket your luggage will be labelled through from Rome to your final destination. There is never customs on exit, so the next time you will see your luggage is in the US, and you go through customs there.
Rome to Amsterdam is internal to the Schengen Area, no passport checks (but the airline will of course need to see your passport for ID checks). You exit the Schengen Area at Amsterdam, your passport will be checked there and if necessary stamped. US immigration will take place when you land there.

Recently, all direct flights from Europe to the US have additional security before boarding, so even if you went through security in Rome, you will do it again in Amsterdam, and there may be a spot check again at the gate before you board.

It used to be additional security check in Amsterdam but the airport was finally reconfigured and additional security check in Amsterdam is no more needed. I flew from Prague to Seattle via Amsterdam recently (November 19th) and went through security check only in Prague. No more in Amsterdam. Passport check and stamp in immigration in Amsterdam. At the gate for Seattle additional questioning about your luggage and so. But that's nothing new.

The last time I went through security for a flight to the US in Amsterdam (September) it was chaos for everyone but the Delta customers. Delta had their own system in place so we did it easy, while hundreds were crushing their way to another check point. Fortunately we were on Delta. I am glad to hear its gotten better as i am going back through in a few weeks. Still i give it two hours if I can..

In September I flew from Atlanta to Amsterdam and then Edinburgh. In Amsterdam I was somehow in the basement of the airport. No security or passport control. All passports were checked when boarding the connecting flight.

Edinburgh is not in Schengen so you did not go through immigration in Amsterdam but in Edinburgh.

Edinburgh is not in Schengen so you did not go through immigration in Amsterdam but in Edinburgh.

Since Scotland is not Schengen, wouldn't that mean you DO go through immigration/passport control in Amsterdam, since you are then leaving the Schengen zone?

No, Robert,
Pissaro is not leaving Schengen zone. He is only transferring there (Amsterdam) from flight from Atlanta to flight to Edinburgh. So no immigration check in Amsterdam. That will happen in Edinburgh which is in Scotland which is still part of UK and that's not in Schengen.

Mrs.EB,
Unfortunately for Shawn it will be the case and he will go through Passport Control in Amsterdam because he is leaving Schengen zone there, but he will not have to go through security again. He will go through security in Rome.