Hi Joe,

You are asking a question that only a lifetime of knowledge could answer! Please do these two things first:

1) Get Fagan's Cruising Guide to Central and Southern California (Amazon) . This is the canonical reference, and one of the best cruising guides anywhere. He will answer every one of your questions about anchorages, conditions, etc. Indispensible.

2) For quick reference and a reliable chart with expert local knowledge on the back, get the Santa Barbara Channel placemat chart collection from Channel Crossings Press (website), making sure to get the SB Channel, Anacapa and Santa Cruz chart/mats. (Sadly there is no Santa Rosa; you probably won't need San Miguel).
 
After you've read Fagan on the Channel and on Santa Cruz Island, and studied the charts/placemats, you'll have all the info you need.

Some local tips:

1) Arrive at the island by noon. Gets very windy and steep water in the afternoon along the "front side."
2) Do choose a big anchorage and swing to one anchor.
3) Don't tuck in too tight against the prevailing westerlies (e.g. at Smuggler's), because the winds usually go east overnight.
4) Do anchor bow in at Fry's if you are forced by a crowd to use two hooks. Better to stay in 40 feet in the outer cove and swing. The winds go offshore because of the canyon.
5) Don't anchor overnight at Scorpion Harbor.
6) Did I mention don't anchor too tight? Get a flopper-stopper and you'll be fine in 40 feet anywhere on the backside.

Have fun,

nick

For sure get BrainFagans book.
I really like Pelican Bay, 2 anchors 30 ft. Much nicer on weekdays than weekends. Holidays are too much for me. Spent New Years there once, it was 80 degrees and flat seas! Some of the best trips we have had were in the winter.Anchor in the middle if possible.Nice little sandy beach to the east for landing. Good most days. Nice hiking. You can hike from Pelican to Prisoner's. nice views.
  
Prisoner's.is OK. lots of eel grass, two anchors. There is good hiking. OK in west winds and swell.  
Little Scorpion is good in a west swell, 2 hooks. behind the rocks. Use your depth finder! 30 ft.
The  Smuggleris is OK but going a shore can be tricky. One hook 15 to 40 ft in sand. Can be rolley. Nice hiking if you can get to shore.
Yellowbanks is next to Smuggles and can be less rolley.
Coaches is a cool place. Don't go there in a south swell. Best in NW swell. Inside only 3 to 4 boats, 2 anchors. outside one hook 40 feet.. Room for 3 or 4 more. Inside, anchor as far to the west as safe., watch your depth. Many more places, I haven't been yet.
Brian'sFagans book is very good because it speaks to which places at good during certain weather. In Fagans book I think he calls a little coves an anchorage . Sometimes a bit tight for me.
Santa Rosa is great, but it's a long haul up to it. Santa Rosa has great diving, because not that many folks make the trip. I like Johnson Lee. Good hiking.
Santa Barbara island is OK for a night if the weather is calm.
 

Joe,
THe others above me on this thread know what they are talking about.  They provide excellent local knowledge.  I've enjoyed numerous trips to Santa Cruz Island, and consider downright amazing, rugged beauty, and unspoiled. Their reference to the book is a must to get.
My favorite anchorages are:
1) Fry's, small, two hooks if within the narrow cove, I like dropping stern hook first, then dropping bow anchor right off the beach. Just a beautiful place.
Coches Prietos:  stunning cresent sandy bay, Nice beach, suitable to set up chairs and an umbrella. Usually easy landing on the east end of the cove. I try to anchor as far east as I can.  Careful that there is a grassy reef just offshore of the east end, and not good to drop an anchor on. I agree that 4 boats is max off the beach, but more offshore on one anchor.
3) Little Scorpion:  two anchors, drop the bow anchor in 25 ft or so just downwind of the rocks separating Little Scorpion and Big Scorpion.  Great snorkling, great caves, awesome for kayaks. 
4) Willows on the back side, nice sandy secluded cove. Not far from Coches, but stay out if weather is rough.
Check out the many YouTube videos of this island.  Here's one of ours from 2008:

https://youtu.be/jCm5y4L94I8

Steven
OMG what a great you tube! I'm in the mood to head to the islands. Thanks
Chuck