How do I deploy multiple stacks in an environment?

Yuu can explicitly name services in juju. So for for example instead of:

juju deploy haproxy
juju deploy mysql

you can just name them whatever you want:

juju deploy haproxy mynewproxy
juju deploy mysql dbserver2

or whatever fits your model. You just need to remember to add-relation based on name after that, so: juju add-relation mynewproxy dbserver2

It's awesome that you're using juju for this, if you want to give us some feedback on how it's working out for you please send a post to the juju mailing list.