As phoenix and carpetsmoker said, it can be managed. I just would like to add that there few more environment variables regarding the use of packages\ports - like place to install.
You can use the advice of carpetsmoker to define the book-keeping information about package to be stored correctly (i.e. /var/db/pkg) and define one place for your "double software" (like /usr/local/mybin and .../mylib etc).
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