Normally, for such type of agreement, the stamp duty is to be paid to the State (as it is covered within the legislative powers of the state).
You may have to check the Stamp Acts of the concerned states, but, to the best of my knowledge, generally speaking it may have to be paid in the state in which the services are to be rendered. This is so because, for example, Section 3 of the Maharashtra Stamp Act, makes the following instruments charges with stamp duty (other states, generally, have similar provisions):
(1) every instrument which is executed in Maharashtra;
(2) every instrument which is executed out of Maharashtra, but which relates to any property situate or to any matter or thing done or to be done in Maharashtra.
In your question, it appears that the services would be rendered in Maharashtra, so it would be advisable to pay the stamp duty in Maharashtra, since it may be covered within the expression “to any matter or thing done or to be done”.
Maharashtra Stamp Act is available at this link: http://igrmaharashtra.gov.in/SB_PUBLICATION/DATA/acts/Maharshtra%20Stamp%20Act%2011.9.2014.pdf
With regard to your second question, you may have to examine the relevant Stamp Act to ascertain whether any specific stamp duty is payable or the general stamp paper of Rs. 100 would be sufficient. In fact, general stamp paper of an amount such as Rs. 100 (which may vary from state to state) is also basically stamp duty, but it is standardized rate for all sundry agreements for which no specific stamp duty is specified. Therefore, it is advisable to examine specific clauses in the Schedule to the relevant Stamp Act whether specific stamp duty for specific instruments is mentioned.
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