1999 Honda civic ex coupe
When removing the distributor I did not mark anything then spined the shaft on the distributor,? How do I figure out how it goes back on the engine?
I can't be specific about your car but in general this is the way you would set up a distributor if the rotor position has been lost...
Remove spark plugs. Rotate the engine with a wrench or socket on the crank pulley and find compression stroke on the #1 cylinder. (You can use a compression gauge or if spark plug hole is accessible just use a finger.) Continue rotating the engine so the #1 piston is at top dead center.
Install the distributor so the rotor is pointing to the wire for #1 cylinder. Reinstall spark plugs and wires, being careful of the correct firing order.
This should get things close enough so that the engine can run. Start the engine. Adjust timing as needed for your model vehicle.
There are youtube videos showing how to R&R the distributor on that vintage of Honda, there may be one that has specific instructions on what to do if you lose timing.
Clever.
I would just add to what @chucktobias said, since you're aiming for ignition timing at 12° (+ or - 2°) before TDC at idle, (Red mark on pulley) set the distributor so it's pointing to the #1 cylinder at around 12° BTC.
That should give you plenty of adjustment at the distributor to "fine tune" the ignition timing.
Then: locate and jump the BRN and BLK wires in step 2 and use a timing light to set the timing at idle using the Red mark on the pulley.

I haven't tried, but I heard that a rough and dirty way to do it is twist the cap slightly back and forth until you hear the engine reach maximum RPM.