If a Business have two branches , Which is best way to register for VAT ? Each branch separate or group ?

You do not need to register both branches separately. VAT registration is required on the main license only. The branches will use the Tax Registration Number of the main business license for their documentation. 

For a enterprise having two Branches it will be the best to Register the Branch having centralised operation.

VAT registration is required if the  value of the taxable supplies exceeds the Threshold limit fixed under VAT Law. Ie AED 375000.00 in case of UAE .

For calculating the threshold limit we have to add all the value of the taxable supplies made by him in one Commercial  license. therefor the turnover of the branches has to be added to claculate the turnover. If the turnover exceeds the threshold limit then you have to apply for registration. ie for the entity as a whole if the branches are under same commercial license.

If the branches are under the different commercial license , them you can apply for registering as at tax group or can get registered branch wise.

the best method is to Register As group.