Welcome to the limits and fun when programming bank oriented scanners. My typical scanner has 10 banks of 100 channels each for a total of 1000. If I program a trunked radio system into a bank, that only required 4 frequencies. In that case, it is definitely best to leave the other 96 frequencies unused unless I plan to use that bank for a second purpose and lock out the first 4.
How you organize banks and frequencies depends totally on what you monitor and how. You must either monitor way more than you want to (because you've filled a bank), lock out most of what you've programmed into a bank (to keep scan time reasonable), or waste a lot of channel positions to avoid the first 2 scenarios.
PRO-95 | PRO-10
| PRO-92 | PSR-300 | PSR-310