Storing covers has been a problem for me. I used to use Showguard cover albums, but I have found that the separators tend to tear, and there is no easy way to add pages in the middle. A few years ago, I found the Supersafe cover albums, which are much nicer in my mind. The albums are a bit pricey, but you can add a bunch of pages to the stock album without overfilling it. The albums come with 25 pages, and each page fits 4 covers. They make pages without a horizontal divider on the page that fit 2 covers (1 on each side) per page. Really large covers go in in plastic sleeves in a binder.
I occasionally search e-bay to find used Supersafe albums, and have had some success. Since new albums cost $20 and up, depending where you buy them, used generally offers a significant savings. With my special cancel collection alone spanning a dozen albums, the albums become a significant investment. One reason my post office openings collection is still not dealt with is that at 4000 post offices, it would require 20-30 albums to hold these.
One issue I have resolved is how to leave blank spots in the albums for missing covers. There are times I am missing many covers in a row, and when I used to get one cover in the middle of a run of 20-30 missing ones it was difficult to figure out what slot in the album to put the cover in. It is made more difficult when the sequence of covers contains sub numbers (for example 1021, 1021a, 1021b, 1022). You need to know how many empty slots to leave, which I always seemed to mess up. My solution was to print markers for each slot. I bought a box of Avery business card blanks, then used MS Word to create a mail merge from my database to the business cards. I now have a business card with the number, date, and description for each cover. I put one in each slot and now I am quickly able to put covers in the right slot. Also, as a consequence of this, each cover i have now has an identifier in the same slot with it.