Please go thru below thread:
Creation of CTC break up in IT 0008 record.
Normally most of the components takes base as Basic pay for calculations.
Basic can be maintained in IT 0008 directly or can be defaulted using Payscale structures and Indirect Evaluation defined in Wage type characteristics.
From that you can maintain HRA as percentage of basic using V_T539J table. You can also maintain it thru IT 0581.
Transport & Medical can also be defaulted using Payscale structures.