I don't have any experience with coir, but typically a mulch is not applied until after seedlings have emerged and grown through at least their first set of true leaves.

If your soil is very loose the drainage rate may decrease after a period of repeated watering (a few weeks to a few months) that allows the soil to settle and compact a bit, and more so over time as the organic material degrades further.

TXEB is right mulch around plants after they pop up. I also think more of your local clay would help with holding moisture. My garden is mostly clay and does pretty well

I am finding that the soil is draining too quickly and the top 2-3 inches tend to be dry (where all my new plants and seeds are) so I am watering often."

Instead of a 2:1 ratio of garden soil to native soil.. Use 50% of your bagged soil and 50% of your native clay soil, or other topsoil.. Clay/topsoil holds much more water then the other amendments you added, you added to many amendments and it's draining to quickly, similar to adding to much bark or perlite to a container, will not hold enough water..

For a mulch, I was considering coconut coir as I have some from when I was vermicomposting."

You could, but it is costly.. Also it dries out quick, not really a mulch... For mulch i would use leaves or straw.. Grow a cover crop in the off season and use the biomass as mulch.. As other mentioned, apply mulch around your seedling, not ontop of them... It also depends on how thick the later of mulch is,whether or not your seedlings will poke through.. Best to apply mulch after seed sprouts..

How much water a clay will hold depends on the nature of the clay. In San Diego I would suspect it is most likely a sodic clay, which tends to pack tightly. That makes the high drainage situation worse than a calcium rich clay as it acts more like a large sand particle than a water absorbing clay particle. If that's the case, then adding some soluble calcium (e.g., gypsum) to the clay portion of the mix may help substantially.

All that said, you already have the soil mixed and planted, so I appreciate it's a bit late. When the season is done consider having the native clay soil tested, watching for sodium vs. calcium. If it's low in calcium and high in sodium, consider taking more of the native clay, amending it with gypsum, then adding that amended clay into the bed. If you just add calcium to the bed it most likely will leach/wash through without having the time to intercalate into the clay particles.

Thank you for all your responses! You are right, it is a bit late - I should have asked this question sooner. The vegetable blend from Lyncso came pre-prepared (top soil, manure and redwood) and I don't really know what the ratio was. We just happened to have some of our backyard dirt (clay - san jose type, no idea what that means) in to fill the remainder - mixed well. So, it is more clay than initially intended.

That said, I also think one of the comments was right on, I did "compact" the dirt a little as we put it into the bed (4x11x18) but it seems to keep sinking. Very easy to press on it and compact it. When I added this last bit of seeds for beans and broccoli rabe, I turned and compacted the soil a little by hand first to see if that will help.

I'll definitely do Fava this winter in some of the bed, but I will also do other winter veggies.

that brings up a question, in an area where continuous gardening is possible, when do you amend? I can imagine by the time the summer veggies are done I will already need to have added the broccoli, cabbage, spinach and other winters.

Buckets sure seem easier :-)

When soil is placed into a container, or raised bed, there is usually a lot of air in the mix and as that soil is wet and the air is removed the soil "sinks", compacts. Organic matter will, to an extent, help keep soils from compacting too much and the optimum amount of organic matter in soils is about 6 to 8 percent.
Coir can be used as a mulch and whether it will prevent seed germination depends on the depth of that mulch. An inch or less will do little to prevent seed germination and growth while a 4 inch depth will.
You can amend your soil anytime, even while plants are growing in it. Mulches can add organic matter as plants grow, you can (carefully) mix needed amendments in your soil as plants grow, you can plunk needed amendments down as mulches so the Soil Food Web will work them into your soil for you.
Those of us with perennials, or that practice permaculture, amend our soils that way all the time.