Assuming you are driving on a rental car - hwy 6 is off limits for you as the electronic toll collection makes rental cars fine anyone who drive the road with a "processing fee" - something around 10 USD in addition to the toll.

The valley road (90) goes through some Palestinian Authority controlled areas like Jericho. I'm not sure how welcomed you will be there with Israeli license plates.

Hwy 6 currently runs between Re'em Junction (other known as Masmiah junction) in the south and Yiron junction in the north (just north of Hadera). If your planned route takes you via the Tel Aviv area (routes 4, 2 and Ayalon - 20), hwy 6 will save you about 60 minutes on regular traffic and about 120-180 minutes on rush hour. The problem with hwy 6 is that it's a 2 lane road and if there is some problem (accident, road work) there can be heavy traffic jams there, although, most of the times the avg speed there runs above 120 km/h (speed limit on hwy 6 is 110 - the highest in Israel). Beware of speed traps as the police is trying to enforce the speed a little more these days.
The toll is billed to the car owner - it is not possible to pay as you go. The toll is determined by the number of electronic toll stations you pass (one after every entrance/exit) with a minimum of 3 and a maximum of 5. The current price of 5 stations (max price) is 20.84 NIS.