Now I have not been through security since late last month (so I do not know specifics on how they are searching the carry-on items now that all this has happened). However, the checked baggage will undergo a similar process to what was preformed before. Remember, the new measures are on Carry-on items only and should have no effect really on checked baggage (other than their will be plenty more of it to screen).
They are searching a second time at the gate to make sure that you have not purchased any items in the airport itself to bring on the plane. If you have a carry on item, be prepared to be searched again!
To answer how TSA searches the carry-on... I flew quite a few times last year and carry-on every time. Since they previously did random searches; I have had my bag searched a few times last year (I tend to carry a ton of electronics as well, with can trigger a search). Anyways, when they do preform the search itself; TSA generally has an idea of what they are looking for (since you just put your item through the xray machine and they found something that will trigger a search). So, they will ask you to open your bag and they will put on some gloves and go to work. Generally, they will also take a swab to analyze to find out if there is any explosive materials in the bag. They will NOT just dump the items all over the table and disregard your stuff. All of the TSA officials that I have worked with in the past have been very strict but respect my items as well.
Take comfort in the efforts being putforth by TSA and the DHS. I know that my travels in the future are going to a bit more cumbersome however it is welcomed hassle to have a higher level of security.
