Dear Sir,
1) At the time of clearance of products from the customs, you need to pay IGST on all imports. Later on you can claim refund of it.
2) Custom duty paid is cost for you as no set-off is available of the same with other taxes such as GST. You can add it in the cost of the product in the software.
3) If you are selling within India, you need to issue tax invoice and charge GST on the taxable value (Cost+margin) as per the rate specified for the beauty products. If you will export then you should apply for LUT (Letter of undertaking) for export without payment of taxes.
4) Apply for registration as early as possible if you have started your business.
Thanks