What type of conformal coating must I use and where must it be applied over the PCB?
You said


  "... So I use clearance and creepage at the PCB design that matches with conformal coating usage. ..."   


DON'T.
6 kV is astoundingly unforgiving.
If you do not utterly HAVE to minimise distances, don't do so.
If you HAVE to, still don't do so! :-) :-(.
Regardless, have your finished actual layout checked by somebody skilled in not carbonising PCBs and circuitry at say 10 kV.

There is seldom any reason apart from cost to not use conformal coating in other locations on the PCB. Components subject to wicking or contact masking may need to be avoided or masked. 

A generally superb conformal coating is Dowsil (formerly Dow Corning) 1-2577 datasheet here

Can be dipped, brushed or sprayed. Rated at 13 kV / mm - but not what you'd rely on as your primary EHT insulator :-). Annoyingly costly in small quantities, but gets much cheaper per volume in litre+ sizes. 

You will need to confirm that it suits your need. The manufacturers are generally highly competent and willing to provide technical advice.
I have no association with Dow Corning apart from being satisfied user of a number of their products.

Related Dow pages here