i did rotate around with the frees at first, but then i just made them kick around shoes. that way I'd still be getting the benefits of walking "barefoot" and still be strengthening my feet but also be able to use my more solid running shoes that have lower heels and more durability. i also ditched anything that has motion control in them and that has helped me enormously as well. i try to get shoes that have lower heel to toe ratios and tend to be under 10 ounces because they work so much better for me and promote a much more natural running motion for me.
i've found that anything with motion control or like orthotics tends to help me for a bit with a particular injury, good for a while, then a new injury comes around, and if the old injury doesnt come back its a new one in its place. eventually i would just get so ladden with injuries that I'd become so weakened in the intrinsic muslce section that not only could i not run without getting injured, i couldnt run without shoes in the motion control area, and it kept getting worse. ended up gradually moving into shoes with less and less support, lighter in weight, lower in heel height and ended up changing my biomechanics entirely. now i've knocked all my old injuries expect for one pesky injury (shins) but thats another reason entirely.
i'd use the 3's for your faster workouts (like tempos, fartleks and moderate runs), if you have access to a track and a pair of spikes then those for speed workouts in the shorter ranges of 100-600m, if you can then longer ranges as well if you think your legs could talk running in spikes for that long, and more of a durable shoe for longer stuff and recovery (anything 10 ounces or under i find to work well, you can alos switch the frees for recovery and the long run shoes for the moderate runs as well). you'll be able to gradually move out of needing orthos once your feet have strengthened enough