When you say you can see the brush marks, do you mean that they're actually irregularly surfaced? I mean - are we talking just a visual effect or an actual difference in the depth of the paint?

If the latter, do a skim coat with lightweight joint compound and when it dries, either lightly sand OR smooth with a large, slightly damp sponge, then apply primer.

As for your own brush strokes - orient the roller so the roller bar leads your motion. If you're moving right, put the bar on the right. If you're moving left, put the bar on the left. The most pressure will be on the roller bar side, so keeping that side on the "front" of your motion will mean the lighter touch side (the back) will smooth out the uneven strokes as you pass over it again.

Now if its not a real issue with texture, just that your seams are obvious - then just prime it again with a good HEAVY primer, using the proper brush techniques, and you'll be fine. :)

Drop Cloths

The most common solution, is to use canvas drop cloths. This has been the choice of the pros for many, many years.

Heavy Paper

36 mil paper is a common choice when working over hard flooring. It provides good spill protection, while also providing a bit of added drop protection.

Masonite Sheets

In higher end homes, where flooring can be quite expensive (and may be installed before construction is completed). 1/8" - 1/4" Masonite sheets can be laid over a medium weight or Rosin paper, to provide good spill and drop protection.