I've fly fished for salmon in the estuaries for 30 years and have compiled some tips for you as far as fly fishing for Chinook and Silvers.
Fly fishing the estuaries will require shooting head systems consisting of intermediate running lines and intermediate 30 ft shooting head, 30 foot type III shooting head and a 30ft floating shooting head with a floating shooting line. With these line systems, I use a 6ft leader of 15-20 pound test on the sinking shooting heads and a 9-12ft leader on the floating shooting heads. These head systems you use will be dependent on the depth of the pool you’re fishing which is influenced by tide activity.
The best way I have found to entice Chinook to strike is by using long slow pulls on the fly line and keeping the tip of the rod low to minimize slack line. This last fall guide season on the coast I had a lot of salmon take the fly on the hang down before I even started stripping the fly in. One thing to remember is after the third or fourth strip just bring it in a recast. Chinook don't follow the fly as much as Silvers do. Those crazy Silvers will follow right up to the boat!!

Some of my favorite Chinook patterns are Orange/Black Comets, Orange/Yellow Hot Shot Comets, Chart/White Clousers , Tater Chip Fly, and Flash Flies.

When fishing for silvers, I use a floating or clear intermediate fly line in a 7-10 wt. I recommend a fast action rod with a good disc drag reel. The best presentation is to cast out to fish you see or a likely looking pool using your floating or intermediate line, then strip the line back very quickly using short pulls. Another method I use is to cast down and across letting the fly drift and sink. Then swing through the holding fish at the appropriate depth on outgoing tide just before low slack. This method often triggers a more aggressive strike as it swings into their space. Once the swing is complete and the fly is hanging directly below you in the current, don’t rush to haul it in. I’ve had numerous fish slam it as the fly hung motionless. I usually use a 9ft leader of 12 lb. test, floating line and a 6-9ft, 12# leader with an intermediate line.
For Silvers, I like the Karluk Flash Fly tied in purple, Alley’s Shrimp and the Spruce Fly.

Hope this will help. One last thing is a boat is very helpful when fly fishing the estuaries.

Rich