Panda Crazy and HIT Catcher both go through the list of Group IDs one at a time. So if you have it set to 1000ms, it will check the first one - wait 1 second - check the next - wait 1 sec - check the next one - and so on. You can have as many Group IDs to check as you want, but the more that you have in the list to check, the less often it will be checking each individual one.
You can basically send one page request to amazon each second. With the new site on the worker subdomain, it seems to be a bit more complicated than that. But ultimately, when it comes to PandA, the limit is still about 1 request per second.
You should not get in trouble or anything for sending too many page requests. What happens is they give you a little error message to let you know that there are too many page requests. This is what we call PRE or a Page Request Error. They are not exactly a good thing to get, but should not get you in any trouble with amazon or anything like that.