I have a stand alone project using a mega2560 and I need to be able to an array saved in the eeprom without using the IDE. Can I do this over serial comm and how do I go about it?
Since the IDE (Integrated Development Environment) is the user interface between the PC and any arduino , it would seem like you are asking "how do I drive a car without a steering wheel ?" The only thing I can think of is that if it is possible to load a program into one arduino from another , then maybe it is possible to load data (any data , array , whatever) into an EEPROM using another arduino. I'm not saying it is not possible but we don't get that question very often. I don't see how you can do it without another uC. Back in the day we used to manually enter the hex codes into the EEPROM programmer with a keypad.. Now , I don't know how it is done. You might be able to build your own EEPROM programmer. That is what your asking right ? How do I program an EEPROM without a programmer ? (the mega is a programable computer that can mimic a programmer using software. If you know another way to get the software into the mega without the PC/IDE then the end result is the same. Asking if you can do it over the serial comm without any way to load the code into the arduino is kind of a (well to be subtle) "perplexing question.
Heres what I'm doing. I have, using the mega, built a electronic automotive transmission controller. Code is done, have thebunit installed in my truck and it "operates" as expected (properly) 
I have a few people interested in having one installed in their vehicle. They couldn't say arduino much less modify code through the IDE. What I am wanting us to build a tuning program that is more user friendly for people on the street. I can modify hex version of my sketch, save it as an .ino file and run that on my mega but only using the IDE. All i need to do is access and modify the eeprom and load the new file into the mega without the IDE.
ll i need to do is access and modify the eeprom and load the new file into the mega without the IDE.
Every section of an (unprotected) AVR can be individually read/written without the IDE.
An old PC is all that is needed... Anything supported by AVRtools: Windows, Linux, iOS. Here is my Windows script:
http://www.hackster.io/rayburne/avr-firmware-duplicator
Good luck with your project,
Ray
save it as an .ino file and run that on my mega but only using the IDE.
Why only from the IDE ? I usually only load a program into my UNO once and then I don't need the PC any more. I could name dozens of programs that applies to but you know what I mean. Why do you need the IDE ?
If you want to have configuration data stored in EEPROM and make that editable via a PC application, the obvious way to do it would be to implement a command interface on the serial port so that the PC application can retrieve the existing values and write modified ones back. Ideally you'd provide a user-friendly front end on the PC. You could do that easily enough using Processing, or whatever other Windows development language and environment you preferred.
I'd suggest putting validation logic on the Arduino end so that no matter how wonky the PC application is, you can't accidentally trash the configuration.