According to these release notes, installing packages via 'conda install' is supported in PTVS, which came pre-installed with my VS 2015. However, I can't seem to find how to access that option. My best guess was as follows:
When I do this, I see the option "pip install waitress" from PyPI. I'm guessing there should be another option there - "conda install waitress", but I don't see it. There is another option in the list - Install waitress. But clicking on that just performs the install via pip, not conda. I confirmed waitress is a package that's available via conda by performing "conda search waitress" from the command line.
I found this bug, and have confirmed the presence of the conda package and conda-meta directory in my anaconda distribution. I also opened the first JSON file in conda-meta and don't see a link to another environment.
I also found this more recent issue, but it appears to just be describing adding a UI element for managing conda packages.
The 'conda install' option appears under the old UI.
See the screenshot here and use the 'Install Python Package' option (the screenshot is highlighting something different). In that dialog, conda environments should have a 'conda' option available.
There's currently no support in Python Tools to create or automatically detect conda environments, so right now you're on your own there.