I normally drive a 7.5 tonner but recently I have been spending some of my time in a sprinter.
This is not good news as the days are invariably long. If I was in my 7.5 these would be nights out.
Perhaps I am being paranoid but without tacho my working and driving hours over the reference periods will be incorrectly low.
I raised manual entries when I started the job but my driver trainer said they are not done there.
My question is should I do a manual entry for the time I spend in the van to better reflect the work I do?
Further paranoia are they using the van to manipulate work and driver times?
In any week that you drive in-scope of EU regulations any none HGV work, for the same employer or another employer, must be manually recorded as other work.
These manual entries can be done either by manually putting the times into a tachograph (not recommended) or recording the times on printouts or charts.
The DVSA require you to be able to provide work records for the last 28 days regardless of whether or not the work is in-scope of tachograph regulations, again these manual records can be put into a tachograph or written on printouts or charts.
The company cannot tell you to break the law and if they do the DVSA will have something to say about it.
Frankly it sounds like the company driver trainer is a nob and should be ignored.
Can van driving be recorded using domestic record sheets 
ROG:
Can van driving be recorded using domestic record sheets
Presumably yes, but it doesn’t seem like the company would have any so the OP would probably need to print some.