NO, you don't have to put the cover back over the springs. It really helps to have a vise to squeeze the springs down then you can ziptie or safety wire them. If you have a way to lift the back of your bike from above ,this trick helps.. Install the shocks with the springs in place, lift the back of the bike so that the shocks are at full extension then have someone push down on the springs so you can install the half-moon locks.
Xnavylfr(CHUCK)