First, you need to specify whether she is covered under Esic or not.
The procedure would be different in both cases. Of covered by Esic, the documentation process is specified on Esic wevsite, you can follow that.
If not under Esic, then you need to pay as per maternity benefits act. (I assume she has worked more than 80 days). She will be eligible for 12 weeks leave, of which at least 6 weeks must be post delivery. You need to pay half the leave amount in advance and balance when she rejoins after leave. She can also take more leave utilising her EL.
In terms of documentation, there is none specified in the act.
So just follow normal HR procedure. Send her a reply acknowledgeing receipt of her application. Inform her that her you will send confirmation after getting approval of MD (or whoever you need to inform) and her reporting manager.
Follow the approval process you will do for normal leave (Except that you will not deny it on ground of not having applied before, etc).
Once approval is done, send her a letter confirming her leave, when she is expected to rejoin, her cheque for advance benefits and any other terms etc. give details of what other rights she has under the act and to inform office of any possible reason by which her rejoining date may change.
I would also suggest HR send a congratulatory or best wishes message.