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Do interrupts set in Sys/Bios and manually by API disturb each other?

Hi,

I started configuring the timer using some API functions from starterware/include folder. During configuration I need to establish an interrupt with the use of interrupt registers. Are these registers the same we use when configuring the hardware interrupts of timers in Sys/Bios? I mean, when configuring one hardware interrupt in sys/bios and second one manually by API gathered in starterware/include, the second one cannot be properly managed by Sys/Bios and there is a risk of errors, am I right?