There are two ways I'd suggest:

1.  Form the wing root fillet from the wing "normally" and let it go through the fuselage.  From there, then do a boolean on the wing/fuselage to eliminate the "inside"

2.  Open a number of polygons on the fuselage, roughly corresponding to where the wing fillet would butt in.  Make sure your wing is open ended on the root side, Perform a  "Connect" operation, adjusting the parameters and maybe adjusting vertices.

In my limited experience, I prefer #1.

I have no doubt others will chime in with more efficient/better methods.