There are a lot of questions concerning the correct use if login, log in, etc.
When speaking directly to an use I would say
You can always change this permission by logging in in the internal download area [...]
because after the "logging in" I naturally would do a very short pause before continuing with an emphasis on "in the internal download area".
However when I wrote it down on the site I'm developing, I didn't like it. The double "in" seems wrong o to me but I don't know how to express that in better way. Could anyone help me here? What about "by logging into the internal"?