1) Copper pours: The polygon tool is a powerful tool. You can use it to outline different areas -- they don't have to be rectangles --, assign different signals (not just ground), and assign different ranks for the pours. I believe it can do what you are asking. Just practice with different shapes and ranks. Use the "i" tool as an easy way to find and/or reassign the rank. I also use the t/b restrict to fine tune the pours. If you can show an example of what you want to do, it will be easier to be more specific.
2) Double-sided, but separate auto-routing: I do not use autorouting, except to get a rough idea of how the board will look. So, I am far from experienced in that tool. But, I did do some testing. If you try to route just one side while components with traces on the other side are showing, you will get a lot of pad unreachable errors. I then split the schematic to top and bottom sides as separate schematics (no board). I then made the board from the top schematic and auto-routed it. Save in temp file and repeat process for the bottom schematic. Save temp, cut and paste schematic from bottom to top. Cut and paste board from bottom to top. I got no errors that prevented me from doing that (e.g., no board-schematic error) and could even overlap components on the two board traces. However, DRC will give overlap errors if you have TH and SMD overlapping, as expected. I did not try to make any electrical connections between the two layers, but I suspect you could add vias after you get the two boards aligned as you want.
Again, it is much easier to give a definitive answer, if you give a specific example of what you are trying to do. Please post at least a part of your design.
John