Hi Devang,
port mode is used when you want to pass through the ATOM circuit all the traffic from one physical Ethernet port to another physical Ethernet port.
The Vlan mode is the same but just for a single vlan. In reality port mode is rarely used most of the time you will use vlan mode.
Both are providing you point to point ethernet connection.
If you want your MPLS network to behave like virtual Ethernet switch providing point-to-multipoint services you have to use VPLS.
Regarding the dot1q mode I am not sure what exactly did you mean. If you are referencing to Q in Q tunnels that is just a way to switch through your network some dot1q tags through another dot1q tag.
Hope that this helps ;)