If I run tor through socks proxy ( installed from sudo apt install tor on linux mint 18 and I browse with the tor browser bundle, does that mean I going through 6 relays? If so how could I configure back to 3 relays on my tor browser?

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No, the Tor Browser will launch it's own tor process by default and both will connect to the Tor network separately.

So unless you've knowingly configured your system daemon instance of tor to act as a transparent proxy and set some iptables rules to enforce it, you will not be creating a "Tor-over-Tor" situation (I.E. you won't be connecting through "6 relays"). They are intended to play nice together.

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