Spacex has not announced that they will use the Spacex Raptor engine to re-engine the Falcon 9 or the Falcon Heavy.
However, if they have an engine that is the same size and roughly the same weight but has three times the thrust then why would they not use those engines exclusively ?
The developmental Northrop Grumman TR-107 engine was built by Tom Mueller, the co-founder of Spacex. It was designed in 2002.
The Falcon Heavy configuration consists of a standard Falcon 9 with two additional Falcon 9 first stages acting as liquid strap-on boosters, which is conceptually similar to EELV Delta IV Heavy launcher and proposals for the Atlas V HLV and Russian Angara A5V. Falcon Heavy will be more capable than any other operational rocket, with a payload to low earth orbit of 54,400 kilograms (119,900 lb) and 13,600 kilograms (30,000 lb) to Mars. The rocket was designed to meet or exceed all current requirements of human rating. The structural safety margins are 40% above flight loads, higher than the 25% margins of other rockets. The Falcon Heavy is currently scheduled for a demonstration flight in Q2 of 2017.
A Falcon 9 Raptor would be able to launch about 60-70 tons into low earth orbit
A Falcon Heavy Raptor would be able to launch about 150-170 tons into low earth orbit.
The extra launch power would leave plenty of margin for larger launches while saving capacity for powered landings (for reuse).
If one third of the engines were used then the raptor version of a rocket would be able to launch cargo similar to the current systems but get an addition 1-2 tons of weight saving per engine that was not needed.
Robert Zubrin had suggested improvements to the Spacex Mars plan
Here is what Zubrin suggested
* Have the second stage go only out to the distance of the moon and return to enable 5 payloads to be sent instead of one
* Leave the 100 person capsule on Mars and only have a small cabin return to earth
* use the refueling in orbit and other optimizations to enable a Falcon Heavy to deliver 40 tons to Mars instead of 12 for exploration missions in 2018, 2020 etc...
* Reusable first stage makes rocketplanes going anywhere point to point on Earth feasible. Falcon Heavy would have the capacity of a Boeing 737 and could travel in about one hour of time anywhere
Using the Zubrin improved plan would enable Spacex to send 40 tons (3.3 times more) to Mars with Falcon Heavy and is without switching to Raptor engines.
With Raptor engines this would enable about 120 tons to Mars.
Developing a Interplanetary Transport class rocket would take even the efficient Spacex about $10 billion of development.
Completing the Raptor engine and the modifying the Falcon Heavy and Falcon 9 to use it would be about $1-2 billion and could be done in perhaps 2 years.
Consider what this revised version of the ITS plan would look like in practice, if it were used not for settling Mars but for the nearer-at-hand task of exploring Mars. If a SpaceX Falcon Heavy launch vehicle were used to send payloads directly from Earth, it could land only about 12 tons on Mars. (This is roughly what SpaceX is planning on doing in an unmanned “Red Dragon” mission “as soon as 2018.”) While it is possible to design a minimal manned Mars expedition around such a limited payload capability, such mission plans are suboptimal. But if instead, following the ITS concept, the upper stage of the Falcon Heavy booster were refueled in low Earth orbit, it could be used to land as much as 40 tons on Mars, which would suffice for an excellent human exploration mission. Thus, if booster second stages can be refilled in orbit, the size of the launch vehicle required for a small Mars exploration mission could be reduced by about a factor of three.
SOURCES - Spacex, wikipedia