In answer to your first question, I think a lot of it is just what you are comfortable with. One additional factor that can play into this is the size of your ACL's within the PIX. My PIX at home, is very basic and I nearly always use the CLI to configure it. I also work with PIX firewalls that have hundreds of ACL lines where using PDM is much simpler.
For you second question, when changing the configuration with PDM, if you remove an ACL for example, the change is reflected within the config. PDM is nothing more than a GUI based interface for the CLI. PDM more or less issues the CLI based commands for you.
In answer to your third question, yes you can switch between PDM and the CLI.
One thing that you may notice with PDM is that some of the commands configured via CLI are not supported. PDM doesn't do anything to those commands other than list them as unsupported commands off of one of the menu items within PDM.
HTH
Steve