If I used Gingerbreak to root my phone will I still be able to get OTA updates and such?
If you root your phone, but *don't* install a custom rom or remove any bloatware, then yes - you will be able to get an OTA update. The problem is that the update will immediately UN-root your phone, and you may not be able to turn around and re-root it. The process of rooting involves exploiting a discovered weakness in the locked bootloader. Motorola isn't stupid - when they issue an OTA update, one of it's primary functions is to close the loophole that was exploited to create root. If they're successful, then the tool you used to achieve root will no longer work, and you'll be stuck with an un-rooted (but updated) Atrix.
What you need to do is decide in advance whether you want to be rooted or not. There are numerous places on this forum and others which discuss the pros and cons of rooting. Spend some time reading them and make your own choice because, in the long run, it's an either/or situation. You can be rooted, or you can get OTA updates.