Can you provide information so we can more easily customize it?  The ee forum was unecessarily difficult to customize and the had to be redone from EE1 to EE 2.  Will yourr aaddon maintain customization in EE2 to EE3?

It depends on the type of changes that you have been made ... eeBootstrap is based on the original templates, revised to be adapted to the Twitter Bootstrap framework.
No changes to the core files has been applied.

You can easily customize using the information that can you find in Twitter Bootstrap Framework