I don't fish a whole lot of Clousers, so I'll let someone who does answer that.
I'm a big fan of eyes on any type of baitfish pattern. Along with flash, they're probably the most dominant feature on many bait fish. Two examples of why I think eyes are important. Two years ago I was fishing off a rock pile nailing small blues. After several fish they quit hitting the fly. When I brought the fly in I found that both eyes were missing. I have two small poppers I saved from my first really fun day of fishing the salt. Again small blue fish but the heads of those poppers are chewed to pieces. You can still see the remmants of the eyes. Take some time next time your fishing and observe some bait fish. The eyes will stand out.
Kevin, I put eyes on all the flies I make, but have had good luck with plain barbell eyes with the natural lead color. I have also used flies where the eyes have fallen off or have been bitten off and they still catch. I believe in most cases the fish see a flash, if it looks like bait then they just go for it. I have had flies that have looked like they have been through a war almost a bare hook and they still catch, but when I have a choice, I alway put a good looking flie on.
Clousers can be used in many ways. I have had good luck stripping them fast, steady hand over hand or just bumping them across the bottom slow. Don't be afraid to try different retrieves. It all depends on the bottom I tend to bottom bounce them more in sandy or hard bottom. Good luck.
My initial retrieve with clousers is to let them sink to the bottom, then hop them slowly along with short quick strips, to work the bottom. If that doesn't work, I'll retrieve the second the fly hits the water, again with short quick strips, to work the middle water. If that doesn't work, I'll throw it out there and dead drift it along the bottom, maybe with an occasional hop here and there (a very good technique to learn!!). If that doesn't work, I throw rocks in the water .
Eyes are not really important. They can help in some situations (like with small anchovy/spearing patterns in clear water), but on most flies they are only there to catch fishermen, not fish. I've caught enough fish on flies with and without eyes that I don't think it makes a difference, in most common situations.
I pretty much exclusively fish clousers and half and half's. A few years ago I would make sure all my eyes were painted, I would even use red thred to represent gills. Then one day my brother wanted me tie him a fly with all differnent colors. No ryhme or reason to the pattern he chose. He caught more fish then me. Since then I tie just basic flies with bar bell eyes (they are cheaper). I have a log for the past 5 years and have seen no difference in the amount of fish caught. I strongly believe with aggressive fish such as bass and blues, if they are there and hungry they will pretty much hit anything.
This past weekend I was out with two other guys all using clousers in different colors and sizes. In two hours fished we caught 6 bass up to 8lbs., two tiderunners with the biggest being over 10lbs., and some large bluefish. No pattern outfished another. They must of been hungry.