Question, is there a way to make a custom loader, I want to change some variables (code)in my program.
The idea would be to create some software I'm thinking like visual basic, make it graphical so anyone can change the code without knowledge of programing or even what an arduino is, then upload the new program back into the arduino.
Or is this just too complicated.
That's technically not an IDE.
What you are trying to do is generate code from a Visual Basic GUI instead of a text editor. So once you generate that code, you have to feed it through avr-gcc to be compiled and linked, just like how Arduino IDE does it, and then use avrdude, just like how Arduino does it.
There are probably better ways of accomplishing this, such as saving the variable into EEPROM and using serial communication to update that variable.