Triton 2 EQ has a max charge rate of 8amps, so setting the capacity to 6500mah and getting a resulting 1C charger rate of 6.5amps should not be a prob.

Reading the manual, it does seem charger allows only a 1C charge rate up to its 8amps max charge rate. If what your're asking is if you have a 9000mah lipo and set it up that way will the charger charge it to capacity even though teh charge rate is only 8amps and not the 1C charge rate of 9amps. That answer is yes, it will charge the lipo to 4.2v/cell regardless.

If your lipo is getting 'warm', thats a sign that it is producing more amps than it is comfortable with. How warm is warm? Generally lipos are chosen so they rarely get above ambient excpet when space and weight dictate the absolute minimum batt (planes and 1/8 buggy). So if 20C is getting warm and warm is less than 110f or so, you're prob ok. A 30C would not get as warm or maybe not warm at all.

Rather than switch to lower C rated lipos to control start power and then have them and the motor run hot, get a Castel link and set the start power to low and then start adjusting "Punch" control til you get it like you want. This would be a lot better way to do it.