Google Apps a great platform for small business as it offers so many features free of charge.
To configure email system correctly to work with Google Apps you have to change the MX records properly. Here is the details for changing MX records of cPanel clients.
Login to your cPanel click on MX Entry

First enter priority and give the first server name (ASPMX.L.GOOGLE.COM) and click on Change button. This will add an entry under the Current MX Entries Section.
Now click on this entry then you will have an option to change it again. Similarly add all these entries in exact order and priority.
| MX Server address | Priority |
|---|---|
| ASPMX.L.GOOGLE.COM. | 10 |
| ALT1.ASPMX.L.GOOGLE.COM. | 20 |
| ALT2.ASPMX.L.GOOGLE.COM. | 20 |
| ASPMX2.GOOGLEMAIL.COM. | 30 |
| ASPMX3.GOOGLEMAIL.COM. | 30 |
| ASPMX4.GOOGLEMAIL.COM. | 30 |
| ASPMX5.GOOGLEMAIL.COM. | 50 |
Google Apps Server will take few hours to reflect those changes.