My understanding is that T5 knowledges are subsets of certain T5 skills; for example, the Pilot skill has Small Craft, Pilot-ACS, and Pilot-BCS knowledges. Knowledges, but not skills, can be acquired through education or training; skill acquisition during terms of service can optionally be substituted with knowledge acquisition, but most of the time a skill would be preferable to a knowledge, since a knowledge is a subset of a skill.
The typical initial progression in T5 skill acquisition is knowledge → knowledge → skill, so a scout character who receives ship skills and is interested in piloting might first select the Pilot-ACS-1 knowledge, then the Small Craft-1 knowledge, then the Pilot-1 skill. At this point, this scout would resolve most piloting tasks at level 1, but small craft piloting tasks and ACS piloting tasks would be resolved at level 2. Subsequent ship skills for which piloting is chosen could either increase the Pilot skill level or any of the Pilot knowledge levels.