Take a look at this site
This paragraph:
"It's easy with most modern transceivers to operate FSK. They provide an input that can be keyed from the PC if you have the right interface. I use MMTTY software for everyday operation and N1MM software with MMTTY in contests. WRITELOG and other ham software will also work. The needed interface is the traditional open-collector solid-state circuit that has been in use since the beginning of ham software development."
If that's the case, the arduino driving a resistor into the base of a transistor with the collector going to the RF equipement is very straightforward.
Or did you want to make the arduino create a pulse train at one frequency and then a 2nd frequency that you send to a transmitter?