Ok. Let's get you set up... I'd recommend opening your .czi files using Bio-Formats - just go to File > Import > Bio-Formats. Too - for visualizing - you can use the Channels Tool. That will let you look at both channels simultaneously or just single channels at a time.
A great place to get started with things is to look at these living workshops. They are a great introduction to using ImageJ/Fiji, as well as how to do Segmentation, which is the direction you are going in your work.
Hope this helps a bit to get you started. You can always post more questions as you go...