Yes you can use. If you mean that for balance sheet you require dollars and for cash flow Rupees this is possible, but if you want to have both currencies in one report eg balance sheet, as per my information this is not possible. As we people mostly use the pirated software so its not possible however if you have bought the original CD from the authorised dealors you may request your required formats and they will make the changes accordingly.
It depends which version you are using of which product, in the UK we have line 50 and MMS both can cope with multi curency to at least some degree. have a look at this comparison
http//www.ledgerservices.co.uk/Line_50_Features.htm