Definitely use the estimated elapsed time at obvious visual fixes, but choose such fixes so that they are at rough fractions of track distance. That motorway at 40 miles along a 70 mile track is near as makes no difference about halfway along track! But the only other marks worth using are 6 minute marks to give a rough idea of position; however, exact 'fractional marks' are pretty pointless unless they happen to concide with something visually significant.
DON'T plan too many fixes, the emphasis is on planning accurately in the first place, looking out, flying acurately and thinking ahead. A student who spends too much time trying to map read, do hard sums or write on a complicated log is less likely to have flown accurately enough to make proportional correction of timing at pre-planned visual fix points. If the student finds that he/she/it is 30 sec late at rthe fix about 1/3 way along track, a corrction of 1.5 minutes to the leg ETA is only valid IF the correct IAS has been maintained on the first 1/3 of the leg. If he/she/it has been wandering about over map reading and hasn't been keeping an accurate speed, the only correction should be to apply 30 sec to the leg ETA and to make any other ETA corrections at the next pre-planned fix point.
Navigation - it can't be difficult if navigators can do it!!