IDE to program Arduino Uno especially internal interrupt vectors
You can do all you need to do in the Arduino IDE.  It doesn't "block" you from doing any low-level operations.  Any other IDE will also allow you to do what you want.

All the information you need to manipulate the "guts" of the Arduino is the datasheet for the main chip - the ATMega328P on the Uno.

http://www.atmel.com/images/atmel-8271-8-bit-avr-microcontroller-atmega48a-48pa-88a-88pa-168a-168pa-328-328p_datasheet.pdf