Upcut bits are the go to choice where having a clean bottom surface or getting maximum chip evacuation is most important. The up cut action of the bit pulls the chips up and out of the cut allowing for maximum chip evacuation. Because the chips are being pulled up this will result in a clean bottom edge of the cut

Flush trim bits cut the wood on your project so that it is flush with the template edge. The downshear cutting edge moves the chips away from the router.