Welcome to the forum, both of you!
Matt, the rafters are required
to sit on the top plate of the two plates or within 1" of the studs below if one plate is acceptable to your local Building Department. IRC 602.3.2X, steel ties used if one plate on top- -- 1-1/2" min. bearing for end of rafter = 802.6. The rafter/tie (every 4') or rafter/ceiling joist connection is critical so the walls don't spread and collapse: Common Nails Required for Rafter Ceiling Joist Heel Joint Connections - Engineers Edge
Pay22, check locally with the B.D. as you are in a seismic zone, same as me. You might be able to raise the joists to stay in the bottom 1/3 of the total rafter rise: Myers Construction Company