You don't mention the brand but, if it's the Sharp CS-930 convection microwave, the answer is yes (use the racks on microwave if that's what the manual says for what you are doing). But this is all fairly new to me, too. We've had this unit for about a year and I'm still referring to the manual. I remember... in the olden days, we didn't put metal of any kind in the microwave... and (for me, anyway) that concept is hard to ignore. So... until you are used to it, refer to the manual often and you should be fine.
Another edit added: Given the other answers that are, apparently, all over the board, I'd say the answer to your question is extremely brand/model specific. For example, the Sharp CS-930 says to use the rack (without removing any other parts) to microwave popcorn.