The options to which you are referring is a standard booking where you select the stateroom, and a guarantee (GTY) booking, where the cruise line makes the selection. The primary difference is with the fare you pay, with GTY's being lower. Also, the GTY staterooms can be assigned anytime from when they are booked to boarding day, with them typically being assigned a couple of weeks ahead of sailing. But you have to wait for your assignment with a GTY.
As mentioned, if there are concerns with motion sickness, mid-ship lower deck locations would be best and would also be best assured if you are selecting them yourselves. However, with the GTY option, once assigned if you are not happy with the location, you can contact whomever you booked through and request a change to a different location within the assigned sub-category. They will be happy to do so based on availability, which, however, is based on booking volume and not assured.
So for the lower fare you take your chances on where the stateroom will be assigned and whether or not there will be available options to move to if you are not happy with the location.