I believe he already knows you...

This sentence relates to earlier on in the book. Throughout the book, Boo has known about Scouts exploits, but Scout has not known much about  Boo Radley.  Over the years, Scout has seen Boo as a scary fantasy phantom-like character, and went on thinking that his personality reflects that as well.
However, in reality, Boo Radley's personality was the exact opposite. All throughtout the book, Boo permormed acts of kindness towards Jem and Scout. For example, he left small presents for them in the hole in the big tree.