The 3 way switch on the back of the router now has no functionality. Installing any tomato firmware willl disable that 3-way switch completely. It no longer has any meaning, it makes no difference which position it is in, and you can now ignore it completely.
Making your new Tomato router into a repeater is not that easy. Tompato firmware has no repeater mode like DD-WRT. If you are trying to repeat another Tomato radio with the same or similar chipset then you can configure them to operate as a single radio using WDS repeating. This is a superior method of repeating than DD-WRT universal repeater.
If you are tyring to repeat a generic piece of shit router with your newly flashed Tomato router then no, you cannot. In that circumstance you could use two radios. One could be in client mode and receive from the afore mentioned radio and then you can run a cable a few feet away and re-transmit using a third router.