ITA - Aircraft Design
The sections MTOW Estimation and Design Diagram document present methods for estimating the size, weight, performance, and thrust of a turbofan-powered airplane. Experimentation with airplane configurations can be carried out online.

A useful material  is described in a book that can be free downloaded here for personal use.

A book on conceptual design of environmentally responsible transport airplane can be purchased here.
The aircraft design process is very complex and it is accomplished with high-cost, high-performance computer hardware, test rigs, flight tests and a lot of other tasks and equipment. 
Due to its complexity and high costs envolved, the aircraft design process is divided into phases: 
1) Feasibility study 
2) Conceptual study and design
3) Preliminary design 
4) Detailed design 
5) Manufacturing 
6) Entry into service and operational life 
Some tasks carried out in the conceptual design phase are outlined in the graphic below: