SA - I'm not really an expert at fishing Ebay, but since I live close by I tend to fish it more than other areas for BM. Here are my answers to some of your questions.
1) What is the best tide?
I think the answer to this question depends on where you're fishing in the bay. For example with an incoming tide I tend to push deeper into the mouth of the river than on an outgoing (I fish W channel). I also try and tuck myself behind natural obstacles where a fish might try and get out the current or chase bait fish (W side of Duwamish Head, N side of Westpoint both on outgoing tides).
2) While trolling, is it critical to scratch the bottom. In the summer we fish on suspended Kings. How does this compare to blackmouth in elliott bay?
I fish the bottom more than the middle of the water column. With that said I've hooked several decent sized keeper BM right in front of the W channel with 75'-90' of wire in 100'-200' of water. I've done the same around Duwamish Head.
3) Do you target concentrations of bait, or just specific areas?
I start with specific areas, but stop to work bait if I see it. As you can imagine there is often bait located in the specific areas I'm working. There have been several occasions where I was zipping along in route to some location and have spotted bait or a rip tide in the middle of nowhere, then stopped and banged a fish.
4) What part of the bay seems to be most productive in winter?
This is a tough one. I start near the Don Armeni ramp in W Seattle (I launch here) then work North around Duwamish Head and West, then turn around and head back South along the shoreline till I get out front of the W Channel. Next I usually shoot over to 4-mile, West Pt and sometimes Meadow. Generally I have found if you catch shakers or find bait, then its a numbers game until you catch a keeper. If I'm not getting hits or not getting bait I move.
I have heard reports of people getting fish at various places on the East side of the bay, but so far have done very little fishing in those areas.
Good Luck...I may see you out there this Saturday if I can swing it.