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My responses/comments are below.
1) After installing 12c ,can i directly add the SOA manages servers to grid ,so it starts monitoring or Do we need to apply patches .
Yes, you can discover your FMW/WLS domain including all of the SOA components out of the box in EM 12c (recommend you go with EM 12c R2 which is up on OTN).
2) previosly ,to enable 11g grid to monitor EBS r12.1.3 we used to apply AMP 4.0 on EBS,is this still needed now in 12c ?
Yes, you will want to go through self-update (or through the offline process) to download and deploy the EBS plug-in for 12c.
3) Can we get most important differences between 11g and 12c grid
Obviously, there are a ton of differences. You can find the majority of those in the documentation in the "what's new" section, so I would recommend checking there first. You will also find that a lot of the new features are highlighted in short 3-5 minute long self-running videos on YouTube in the OracleLearning and WebLogic YouTube channels as well as off the EM OTN pages.
4) Most of the documentation asks to go to update functionality in grid for plugins ,can't we manually download them and apply to the agents ?
You can download plug-ins and apply them in an offline manner as well per the documentation on OTN, but if possible, the best practice is to use the self-update feature which simplifies the effort and provides a more fluid version tracking system through the UI. Regardless, you can use the offline approach as required given your environment needs.