With the table version, make your slices. If you want some slices not showing in HTML, use the Slice Select Tool and hold Shift key to select the slices you want visible. When you go to File - Save Optimized As:, Save As Type: HTML and Images and in Slices choose Selected Slices. By choosing Selected Slices, Image Ready will create the HTML code with spacer gifs for the Unselected Slices.

Making transparent areas on a GIF is very easy to do. Same as making a GIF. First you must make sure to change Background to a Layer in your layers palette. You can do this by double clicking on Background (in layers palette). Layer Options pops up with a name of Layer 0. Click ok. Using the magic wand or marquee, make your selection(s) you want transparent and hit delete key. You will see the grey/white checkerboard showing through. In the Optimize palette (top right) make sure you select GIF in settings then go to File - Save Optimized As - Save.