Special marriage

I suggest for both of them, special marriage Act.  For that they need not to come to India.  They can approach the Indian Embassy/consul in the country where they are living and can get the marriage registered there.  For getting the same done in India, at least one month stay is required for both of them.

sir if at all they marry here in india under muslim marriage act after ...the girl getting converted to muslim.can it b converted into the special marriage in anyother country @ indian embassy?

right now they live in different countries?

A marriage solemnized as per Muslim rites and customs, can be later on registered under Special Marriage Act and after the registration, in respect of post-marriage matters, the provisions so SMA is applicable and not the personal law of the religion.  In India, for registratin of marriage from the date of application to the date of registration of marriage, 30 days clear gap is required as per law.  But, I heard, some embassies released their own rules, where 90 days stay in that particular country is mandatory for registration (This point requires to be confirmed by embassy, where registration is proposed to be done).