All flight time should be counted in the Total Flight duration column. This at least is the case in the US, and I beleive in at least most if not all, other countries.
For example, If you are a student pilot receiving flight training on a Cessna 172, you can log this flight as Total time, as airplane single engine land time, and as flight instruction received time.
If you are a student pilot flying solo in a C152 youll write: Total time, ASEL time, PIC time, and Solo Time.
If you are flying the same flight at night, you can log all the above
PLUS night time.
Check the regulations for your country. I know that in some countries, you can not log PIC time while the instructor is flying with you, even if you are a certified pilot receiving training for a higher rating or certificate. At least in the US, where I fly, you can log this time as PIC (for example, when training towards an instrument rating)
Hope this answered your question.
