Say I write a program for Arduino that involves timing. (Milliseconds). Timing is not required to be very precise. It could be off by 100 milliseconds and I wouldn't care. If I use the internal 8mhz clock on a Breaduino or the 16 MHZ crystal external on Breaduino, or a real Arduino with 16mhz Clock, will it make any difference in how I write the program. Will it effect any speeds that were written to have specific delay in milies?
As long as you have defined different entries in the boards.txt file for the different CPU speeds then it should work reasonably well. So the entries in the boards.txt file should match your fuse settings and CPU speeds, then when you select it in the IDE it should compile for the correct speed adjustments. Keep in mind that depending on the core files used it may not have proper support for some CPU speeds.
I did not know there was a setting for this. I will try to find something.
Edit: Not finding anything. Did you just mean to make sure I use the right boot loader for the intended speed?
I don't see any setting in Arduino IDE to change CPU speed etc
From the IDE the board selection identifies different Arduino board types and includes speed settings for that board. So when you compile and upload the sketch it adjusts timing correctly for the CPU speed for that board type. If you create your own custom board type (Breaduino) then you will need to add that type to the IDE to correctly identify the CPU speed that your board is running.
If I just want to use the microelectronic by itself on a pcb with or without a external crystal...How do I designate that when programming it?
You can find some guidelines here, http://arduino.cc/en/Tutorial/ArduinoToBreadboard
Scroll down to the section "Minimal Circuit (Eliminating the External Clock)."