If you always want ae to become æ even in words like æroplane then adding OpenType glyph substitutions is the way to go. FontCreator doesn’t currently support glyph substitution so will have to use a third-party application like MSVOLT to do that, or see this tutorial thread on Adding OpenType Features.
Remember that most applications do not support OpenType glyph substitutions so these fonts will not work everywhere.
The other approach is to use autocorrect or customised keyboards for this.