Yes- you need to replace the round spark plug rubber rings too.
I had to do the valve cover gasket for my 94 Accord (same engine as yours). I got my valve cover gasket set at Autozone and it had the spark plug rings included. My engine has 253K on it and it is still running great.
I left the plugs in when I replaced mine.
If the oil is still pooled down there around the plug, you can try to stick a rag down beside the plug to soak it up (while the valve cover is off), and then you may need to pull the plug out and let the rest drain into the cylinder.
If the plug is nearly submerged in oil, and you the oil let it drain into the cylinder, you may want to crank the engine without that plug in place and let the engine blow the oil out the plug hole rather than risk hydrolocking it and bending a rod. It may be an unrealistic fear due to the small volume of oil, but I'd hate to find out the hard way.
The only weak spot that I have read about for these engines is that the cam and crank oil seals can harden and leak quite a bit as they get old, and there is a balance shaft seal that can actually pop out and you can end up with a massive oil leak.
http://bernardsblog.blogspot.com/2008/09/honda-balance-shaft-seal-pop-out.html
There is a fork shaped metal seal retainer that was made after the problem came up, which solves the issue (it holds the seal in so it can't ever pop out). There is a good chance that this fix has already been done to your car if the balance shaft belt has been replaced.