Salmonlips - In 1995 I spent my Sabbatical in Tillamook bay in a 24' bayliner Cierra Classic. Almost 3 foot of draft with the outdrive down, over 6,000 lbs of boat. I had a merc 9.9 kicker with an autopilot which really helped me out. Was there for 40 days, fished about 30 days ( a lot by myself) and only got on the ocean 3 days. The bar/ocean was UGLY that year. Sooo.... I explored the bay. I went clear up into the middle bay to the picket fence, across the flats at high tide, around the sandbar above crab harbor into the west channel etc etc. Bumped a lot of sand bars, but I got off every one and didn't spend the tide or the night. Get a good chart, use your head about the tides, follow the "sticks" where the channels have been marked and follow the other boats. Watch the depth finder like a hawk and pick your way around. Oh ya - GO SLOW, use the kicker. Be prepared and alert, it's tricky but you can do it. I won't argue about the upper bay advise from Trollin (have never fished that end), and I wouldn't try to get there from the ghost hole at any rate. But... you can do a lot of exploring and have a good time doing it. I caught most of my fish that year in 3-5 feet of water on the flats (incoming tide) using the big roll trick.
The best part was seeing all the guides faces in their flat sleds, sitting in the rain while I'm enjoying life under the hardtop. Oops - fish on - gotta go