What is the best way to compensate for stringing beads that have different hole sizes?
String large-hole beads over smaller beads to keep them in line with the other beads in your design. For example, string seed beads the length of the bead with the large hole. String the large-hole bead so that it covers the seed beads, they will then fill the hole of the larger bead when strung. Be sure to choose seed beads with a slightly smaller diameter than the diameter of the hole of the large-hole bead you want to string.
Another way to keep large-hole beads in place is to use very small rounds or bicones, which fit the style of your design and are only slightly larger than the bead hole of the larger beads. Part of the smaller bead will fit within the hole of the larger bead, keeping the larger bead in line with other beads along the strand.