alias atom='atom && grunt watch'
More seriously, I don’t think there’s any binding with projects build systems yet. This will probably come in at some point, but dealing with make, rake, cake, grunt, gulp, etc. will require a serious groundwork in the core.
About your second question, I think the first thing I install in my terminal when I setup a new computer is a terminal multiplexer, so I’m not really affected by having three panes with my watchers in a single terminal window (if having many terminal windows is an issue), and by experience I know I will frequently restart the watcher in a project when working on it.
Looking at the problem, I found that module: grunt-subgrunt that you can supposedly use to setup a master project and running tasks of its sub projects from the master gruntfile, but as watch tasks never terminate themselves I wonder if it’ll works. I have not tried it yet but if it works sequencially then it’s a dead end. But if it works, you can put your package’s plugins directories in the main package (and listed in its .gitignore) and you should be able to grunt watch your package and all its plugins at once.