If you are familiar with the cdj-100's there should be no problem in operating the cdj-1000's, just spend an hour with it and try everything out.
Just like the cdj-100, the cdj-1000 has a pitch fader, a cue button, skip buttons and a play button, so there should be no problems in just playing tracks like you did on the cdj-100

There are a couple more 'extra's though:
Hot cue is really easy, you have 3 cue points that you can store. Press hot cue and then one of the number buttons, and you recorded the spot on which the track is paused. Press hotcue again to set the cue buttons in 'play' mode (they will turn green), and when you press a number, the track will be played exactly from the point you recorded the cue point.
You can also put a sd memory card in the cdj-1000, and it remembers all your stored cue points for all of your tracks of all your cd's. Switch cd's and it recognizes the cd instantly and immediately has the cue points ready for each track you select.
The main difference between mk2 and mk3 is that mk3 supports MP3 cd's, when you have a CDR with different albums on it located in seperate folders, there are small 'left' and 'right' buttons which you can use to browse trough the folders. Use the skip buttons like you would use it on a 'normal' audio cd.
The jog shuttle on the cdj-1000 is a bit more advanced then the one on the cdj-100, put it in 'cdj mode' and it behaves just like a normal cdj-100 shuttle. When you switch to 'vinyl mode' however, the shuttle splits up in 2 parts: The side, with which you can pitchbend (like you would do on a vinyl turntable by putting your fingers on the side of the platter), and the top, which behaves like putting your hand on the vinyl record and 'scratch'

Pretty straightforward.
These are the basic things you will be using the most, obviously there are more, but for those things they invented the manual :P
So I would say, just take your time and 'fiddle' with it a bit, try things out and find out what each button does, it's not that hard
