How do I ensure that all of my beads become labeled with biotinylated biomolecules?

All of the beads should be attached to antibody if you use a 10 to 20-fold molar excess of biotinylated product. Washing away unbound antibody is straightforward – you can magnetize the beads and wash them to remove unbound antibody. You can repeat this a few times, it is not trivial to remove any unbound beads from bound beads.