If you have some legacy projects that run on Python 2.7, that does not mean that you should have Anaconda 2 and 3 installed at the same time. Although this shouldn't cause any significant problems, it can be confusing and irritating to deal with environment variables and whatnot. (I may be wrong on this - there may be compatibility problems that I am unaware of!)
Instead, what I recommend is to install only Anaconda 3 and use conda's virtual environments. Virtual environments allow you to create an independent project environment with different pip packages, package versions, and most of all different Python versions. Anaconda supports virtual environments in conda, and you can easily make a Python 2.7 environment in the console with
conda create -n Python27 python=2.7
This will create a virtual environment with the name of Python27 that runs Python 2.7, and you can run and manage all your legacy projects within this environment. That includes running files, Spyder, Jupyter Notebook, etc. You can activate this environment with:
source activate Python27
Even if you find a workaround for your problem with different Anaconda distributions for now, ultimately you will be using virtual environments. So I recommend doing so right now!
EDIT: The official Anaconda documentation also explicitly mentions conda environments as a way to install multiple versions of Python.