OK. Be prepared to pull your hairs out one at a time, feel like walking out of the office, crying. But in a few weeks it will get better and it helps if your IT people are worth a damn (ours also moonlight in Geico commercials).
BUT don't let the ATS people tell you it's all going to work out fine. I'm sure you're hearing about plenty of things getting fixed "under the hood." If you have issues while the ATS people are there (I'm assuming they are training you guys, which is what happened here) don't let them get away without fixing them. The ATS system is NOT very compatible with either Adobe product, and it will be (still is) at times a huge pain in my ass.
I will say that despite all the problems that will arise, if I had the choice to go back to Quark and ATS, I wouldn't take it. With the Layout function in InCopy you can have your part-timers and agate folks filling in copy to fit a news hole on the page. It really works great for big prep nights when the main layout person has better things to do than squeeze a couple grafs or shave a few sentences. It also eliminates a lot of the layout guesswork you had to do in Quark, since now a writer knows exactly how many lines you need them to write.
That said, nearly all the problems you will face from now until you leave that paper will be when ATS is communicating with InCopy (and sometimes InDesign). BTW, THE PARAGRAPH COMPOSER SUCKS A BIG FAT ONE. If your system works like ours, you’ll be close to deadline and your story in InCopy will say that it’s copyfit and when you save it and close it will be two lines short in InDesign!! It’s random when it happens. BUT THIS HAPPENS EVERYDAY, ALWAYS HAS. You just learn to work around it like all the glitches with ATS and Quark.
It’s a love-hate relationship. I could go on for hours. Please PM me if you want more info. Perhaps we should start a support group …