Most often, since the MOT relies on spontaneous emission, the atom may decay to a different electronic state(for example, a different hyperfine ground state) which cannot be cooled by the cooling beams. A repump laser beam, or multiple repump beams, tuned to the transition(s) of the untrapped electronic state(s) is used to bring the atoms back in the cooling transition.
Most alkali atoms have two hyperfine ground states. While one of the ground states is used for the cooling transition, a repump is required to bring atoms which decayed to the other ground state back into the cooling cycle. In Sodium, one has the S1/2 F=1 and F=2 ground states which can couple to the P3/2 F'=0,1,2,3 excited states by the 589 nm D2 transition. The F=2 to F'=3 transition is used for cooling, while the F=1 to F'=2 transition is used to repump the atoms that decay into the F=1 hyperfine ground state.
Using laser cooling with 3 perpendicular pairs of intersecting beams, termed an optical molasses, the atoms can be cooled down, but they cannot be kept in place deterministically. Slowly moving cooler atoms can drift out of the center as they will have too low a velocity to be in resonance with the red-detuned beams. In a MOT, magnetic fields are used to create a force field whose strength depends on the position of the atoms. Magnetic forces are not used in the MOT whatsoever. It is the spin-magnetic field coupling causing Zeeman-splitting that gives the force. As an atom travels farther and farther away from the magnetic field minimum, it's energy levels are split more and more. As the levels are split, an energy level of interest gets closer and closer to the laser's detuned frequency. This improves the laser cooling efficiency. As such, a "space dependent force" is indirectly created.
The anti-helmholtz configuration of the coils is a pair of two current loops with opposite current. This is important because the magnetic field created by the two coils of current will have a "zero-point" in the middle between them at which there is no field--more importantly, a minimum in the field, and thus a minimum energy state for the neutral atoms. Any particle moving out (axially or radially) from this point will experience a magnetic field gradient that causes the Zeeman splitting necessary for the MOT to function fully.
MOTs tuned to different atoms can measure relative quantities of different isotopes.
Foot, C.J. Atomic Physics. 2005 Oxford University Press.
C. Monroe, W. Swann, H. Robinson, and C. Wieman. Very Cold Trapped Atoms in a Vapor Cell. Physical Review Letters volume 65 number 13 page 1571. 24 September 1990.