In our current business we require our customers to fill out and complete an application that has a few questions and requires a signature every year. Currently we have filemaker export a pdf then email that to the customers. This of course isn't editable and has to be printed out, filled out and mailed back to us.

I'm looking for a better solution but I'm not sure which direction to go. I'm looking at either using something like pdf manipulator to create the editable pdf or creating a web form with filemaker than can be filled out online but I'm really inexperienced with pdfs and with filemaker's online features.

What is the best solution or what would you recommend? 

You can create editable PDF forms, although I'm not sure FileMaker can create those. The big question here is why do you need the signature? If this is for legal reasons, then an online form or editable PDF is probably not going to cut it as they can be forged too easily. In that case you probalby want to look at online services than can digitally sign documents for you (I've been asked to fill out a few over the years, they appear to be legally sound afaik).

If not for legal reasons, why bother with a signature? You could create a webform with authentication and accept that as a 'signature'. You could ask some security questions only the rightful owner knows, for verification.