Hello,
Even if your users run MRP manually the problem is temporary and ATP will be refreshed when ATP load job runs.
What is the business scenario that users cannot wait for scheduled MRP and instead run MRP themselves manually ? In our case users do not run MRP manually we have daily MRP which on completion triggers ATP load.
In your case yes then you may have to either inform users to run transaction ACBD manually for the material for which they ran MRP so that ATP is also updated or you can make an enhancement in your system to publish an event when manual MRP is run and that event can trigger an ATP load for the specific material for which MRP was run.
Below SCN document might help, it is not really relevant but can help you.
http://scn.sap.com/docs/DOC-58274
Also please check all SAP notes linked to " 99999 - ATP server: Installation and sizing"
Hope this helps :).
Best Regards,
Ameya B.