Firstly have you given your W8BEN (I do not know the exact form number, but we normally submit this form to a US Payer if we do not have any setup in USA). This form is required by payer in order not to deduct witholding tax. having a bank account or fax / telephone in USA does not make you have a PE in USA. But if you have a fixed address in USA, for business income only USA has the right to tax as per DTAA. For Professional Fees and Included services both have right to tax.
In order for your business income not to be taxed in USA, you should not have a PE in USA. However, if USA law specifies that tax should be deducted on your included professional services that you have rendered it will be deducted and if your Form W8BEN is accepted, then they may not deduct witholding tax if your income is not to be taxed in USA.
Now whether your income has suffered tax in USA or not, you being resident of India, your global income is taxable in India. Say you received 25000 dollars in the year in USA and 5000 was witheld for witholding tax in USA. The Indian Government will take your income as $ 25000 only. Finally after all your allowable expenses for generating this income, it determines that your tax liability is USD 5000 for Indian taxes on this income, you pay nothing as you get a relief for USA witholding tax. If your Indian tax ON THIS INCOME works out more, you pay the difference. If it works out less, you get back NOTHING from India.
Sounds simple? Yes, but cumbersome in practice. Please get your CA to fill the return. Even if you have to compulsorily file it online, ge t him to generate your xml file for uploading.