Hello Anon
1. Proficient with X
This usually implies that X is an instrument, e.g. "proficient with an axe", "proficient with firearms", etc.
2. Proficient in X
This usually implies that X is a skill or a discipline, e.g. "proficient in using Google", "proficient in martial arts", etc.
In your example, "proficient with technical manuals" seems to suggest that the person uses technical manuals as an instrument (perhaps for hitting IT helpdesk operatives with).
On the other hand, "proficient in technical manuals" suggests he has a wide knowledge of technical manuals, which is probably not your intended meaning.
Perhaps "proficient in writing technical manuals" would do the trick!
MrP