In the "flight rules" box. So you'll either have 'V', 'I', 'Y' or 'Z'. If you include Y (IFR becoming VFR) or Z (VFR becoming IFR) then you put in the route box the point at which the flight rules change, along with how the flight has changed, separated by a '/'.
So, to use your example: EGLK N0120F040 DCT SAM/N0120VFR DCT MP
As for when to file - your assumption is right. Have a read of the first 3 pages of
Filing Flight Plans which provides guidance.
CM