Although I've not used FMPro migrator 'in anger' I suspect that it's very like the FMP site assistant... If it will deliver exactly what you need, then it will be an excellent choice, but as soon as you want to change anything, it will be significantly more convoluted than if you'd built your solution from the ground up and understood how it worked...
YMWV (will ;-)
I've never used it, but I believe FMPro Migrator creates a SQL database and web app out of your FMP database.
Make sure it can do what you want it to do before you go down that route.
And as Steve says, it would likely be pretty hard for you to modify if you don't have strong(-ish) PHP skills.
: database design
: web development