Apply wood filler before you start your second sanding session, by applying the wood filler, the edges would appear to be connected with each other, it prevents gaps that can ruin your enclosure's design and appearance. Later on you will sand the enclosure for the second time with the wood filler all dried up, doing this could result to having smooth edges and flat surfaces.
REMINDER: It is fine to has an excess layer of wood filler because later on you will even out the enclosure's surface by using your electric sander.
Summary: Fill the gaps and cracks using your wood filler (putty).