Hi steveme,
Welcome to the wonderful world of mileage running

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Before you actually start taking mileage runs, you've got quite a few other questions that you seem to need to be answered. Living in CLE, CO is the biggest carrier & given the fact that you plan on doing a lot of work travel, I imagine that CO will be your company's carrier of choice. Being from CLE, you'll have a LOT of other OnePass elite members to be "fighting" against to get upgraded. You'll also have a 50% EQM earning on lower fares (unless purchased at CO.com - what's your company's travel policy). Given this, CO may not be the best choice for you. From what I understand, CO has a history of having ridiculously high prices from their hub cities & discounts from hub cities are usually less.
I live near IAD - one of UA's hubs. I'm a NW flyer & I get upgraded about 90% of the time because their aren't as many NW elites in DC. If UA offered free upgrades, I'd rarely get them if I was a UA flyer because of all the UA super-elites in the area.
I think you may be able to get a little bit better input on which program you'd like to join from the TravelBuzz forum as they would be able to better advise you on a frequent flyer strategy for your area. Once you've determined which program you'd like to go with, feel free to come back to the Mileage Run forum to help understand how to do the actual mileage runs. You may also want to change your title (or request a moderator to change your title) so that it better reflects the questions you are asking - which FF program is best for your situation?
bhatnasx
Moderator, Mileage Run