I was there last Saturday, and it was a very low (maybe minus) tide. It was a small boat that doesn't draw much. We put in at Carnahan (end of 5th Street in Tillamook). There's skinny spots at low tide, you just have to be careful and watchful (having a partner to watch out the bow doesn't hurt). The Hewes wouldn't work up in the river, DB would be fine. There were bigger boats that launched at Memaloose -- I think they had to stick to that area (which includes the Picket Fence) until the tide came up a bit (again, very low tide). At low tide, it's a fairly shallow run out to Bay City and the Ghost Hole, but your DB would have no problem. You can troll all the way, but it's a shallow run. From the end of the Fence, I'd reel up and head east to Bay City (you'll see where people arer fishing). From there, you can troll all the way through the Ghost Hole, up to the point. Actually, you can troll all the way up to Garibaldi. Anything lower in the bay than that can get rough, so probably not the best place for the DB, fine for the Hewes. The Hewes can fish along the insides of the jetties if it's not too rough (or outside along the South Jetty, if you've got cajones). It's not a horribly long run from Memaloose to Bay City/GH.
So, if it's not a super-low tide, you can launch the Hewes at Memaloose or Garibaldi (I hate that launch. And the lack of ramps on the bay sucks). The DB you can launch at Carnahan and motor out (say hi to the 200 guys anchored in the Hospital Hole, since the bank is closed -- dropping an anchor there used to get you shot), or launch it at Memaloose, and follow the crowd along Picket Fence. The trolling lanes will be pretty obvious, since it's not exactly a secret fishery.
I'm thinking maybe first time out, use the DB, and get the feel of the layout, then the Hewes once you're comfortable.
Hoping I can get out there this week, myself. Been pretty slow out there.