Test the shower pan for leaks before installing the shower drain. If the pan is not water tight, the weep holes will not do anything to prevent leaks. Fill the shower pan with water overnight and check for water seepage in the morning.
Install the shower drain in its slot in the shower pan. Cover the weep holes with the tile spacers. Don’t jam them into the holes, just place them on top.
Mix and apply the floor mortar to the shower pan. Angle the floor slightly so it slopes toward the drain. Keep an eye on the tile spacers; if you knock one out of place with the trowel, check the weep hole to be sure no mortar got inside of it. Scrape out any stray mortar you see.
Leave enough space at the drain to fit the tile you’ve chosen between the top of the mortar and the bottom of the drain. Leave the tile spacers in place as the floor mortar cures overnight.
Remove the tile spacers before you lay tile in your shower. Tile can cover the weep holes; it won’t seal them shut just by lying on top of them.