i need to save a 3 digit # and a 4 digit # in an array
The number of digits in the numbers is irrelevant, as long as the array type is correct (int, not byte).
array[3 digit #] = (4 digit #)
Does this mean that you need an array whose size is somewhere between 111 to 999?
using the EEPROM
On which Arduino? You may or may not have enough room in EEPROM for a 1000 element int array.
I am recieving this data using serial GUI.
How? The Arduino doesn't have the native ability to display a GUI.