It's fairly straightforward man-- I'll get Matt to work out a better writeup for it though. Just go ahead and go with the 3.0.3 firmware if sequential is in your future. Then it's really as simple as this:
Install the Sequential Module in your DIYPNP. This plugs in to the mainboard. (you first solder in the header to the mainboard so it has something to plug into).
Now, you have 4 fuel outputs instead of just 2 like you had before. So, you wire them up to your cylinders in firing order. You have four outputs, numbered 1,2,3,4 and firing in that order. And you have four cylinders, but they don't fire 1,2,3,4, they fire in a different order, 1342 to be exact. So you match this up.
Wire output 1 to cylinder 1.
Wire output 2 to cylinder 3.
Wire output 3 to cylinder 4.
Wire output 4 to cylinder 2.
Now, you just enable sequential in software, and tune the settings. This is done in the 'Advanced > Sequential Injection' menu. There's really not much to 'tune' here unless you're just dying to tune something, you really only need to set a few base settings and then just let it rip. As I just tuned a SC'd 99 Miata with Sequential Injection using this module and code, here are the settings I used.
This will start the squirt right at intake valve opening during cranking, and 10 degrees before it opens when running.
More information on how to further adjust these parameters if you want to fine tune further is here: Sequential Injection Code for MS2
Otherwise, what I posted above will work fine for your Miata, and likely for most MPFI vehicles. I suspect to fine tune the timing further you will need the aid of a four or five gas analyzer to see the exact benefit of different valve timings. Note you also now have individual cylinder trim tables for VE and can fine tune fueling for each cylinder. To tune this you'll need one of three things, individual widebands in each runner of your headers (expensive), individual EGT in each runner (less expensive), or a handheld laser pyrometer to check each runner from the outside (downright cheap and somewhat questionable).
There, I pretty much wrote it up. Hey Matt, wanna add anything I missed and turn this into a writeup for the site?