Well since it started before obviously something got screwed up check to make sure everything is plugged in correctly and pray that maybe you just blew a fuse go to the fuse boxes and see if any ignition fuses are blown.

You have 3 wire COP coils. One wire is 12 volts. One wire is Ground. One wire is the Triggering Signal from the computer.

So all you have to do is select 1 coil and test the 3 wires. See what's missing. 

Here's a wiring diagram of your ignition circuit.

The actual wire color abbreviations are printed on the diagram.

I just made, 12 volts power RED

Ground GREEN

Triggering Signal PURPLE to simplify it.

CLICK TO ENLARGE

So pick a coil, any coil.

If you don't have 12 volts on the BLK/WHT wire at the coil connector then follow the wiring circuit back (checking any connectors) back to the Ignition Coil Relay in your underhood fuse box. (this is the part of the circuit I highlighted in RED)

Check that the relay is good and then check to see if power is getting to the relay sockets 4 & 2 from fuse #18.

Here's how to do that: (you have to click the Grey buttons to open up the images)

http://honda.automotive-manuals.com/civic-2006-2009/A00/HTML/40/SNB6E40A26100034112FAAT00.HTML

If you have Power on the BLK/WHT wire at the coil, then check that you have Ground on the BLK wire at the coil connector. (this is the part of the circuit I highlighted in GREEN below the ignition coils)

If you have Power and Ground going to the coils then you have to check for the Triggering Signal on the 3rd wire of the ignition coil.

Here's how to check Power, Ground, and Triggering Signal on a 3 wire COP ignition coil

https://easyautodiagnostics.com/misc-index/cop-ignition-coil-tests-1