I want to dual boot Ubuntu and elementary on the same drive, but keep the home, swap, and boot partitions separate. Will this prevent applications from accessing the other OS (I want to isolate Ubuntu so that it's "clean")? How can I set this up so that I don't accidentally install Ubuntu into the elementary partitions? For reference, I'm using the "something else" option for both installs where I create my own partitions.
There's nothing you preventing you from creating separate partitions for your data using
gparted or the partitions tool in the Ubuntu/Elementary installer. You can't prevent yourself from overwriting a partition, but you can give it a helpful volume label so you know what each partition is. If you'd like applications on the other OS to not be able to access your data, you can use the "Encrypt my home folder" option when prompted by the OS installer - just keep in mind this also means if you ever forget your password, you won't be able to recover your data without the key provided during setup, so proceed with caution.