PICBasic uses NO Hardware features of the PIC (besides Stack, RAM and Codespace of course) with a few exceptions...

ADCIN will use the A/D Converters
HSERIN and HSEROUT will use the USART
HPWM will use the CCP Modules and note that TMR2 is usually associated with timing those (but best check the Datasheet for your PIC)
The USB Commands will use the USB Module

otherwise all the TIMERS. SPI module, Comparators, OP-Amps are free for your use. Naturally if you don't use those Hardware Commands of PICBasic then those PIC features are free to be driven by you howsoever you please. PAUSE (since you mentioned it) is a software timer.