Multiple Python Package Repositories aka Managers an issue?

I was trying to get Nose to work with Pycharm without adding yet more package managers. It seems though that the packages list function is as follows, do I have it right?

1.Pycharm has its own repo.
2.On a mac, the mac has several repo locations.
3.If I have vagrant/virtualenv, I have my own repo, which I should be able to include.
4.The repo URL used is only visible by tooltip, so I cannot see at a glance which packages are being used from which repo.
5.I cannot change the order of seeking of packages unless I delete all the existing repos and then put mine at the top.

I hate like the dickens to have so many repos floating around, and yet for a VM use I definitely want to separate those items. Am I missing the boat on a best practice workflow here?
thank you!

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