Depends on how you want to set up the filtration, and how your boat is currently plumbed. If you have a single tank-to-motors fuel line, and split off to each engine, you can use a single filter in the main line, in which case you'd want a flow rate well beyond the sum of the burn rate for both engines.
If you have a separate fuel line running to each motor, you'd need two filters, one on each line, that exceeds the burn rate of a single motor.
If yours is the former setup, note that there's nothing that stops you from having a filter on each motor feed (gives you a chance of running if one filter packs up.)
Usually, the filters' flow rate is way higher than your motor will ever burn. To a point, a larger rate is better, as filtration (the filter actually picking stuff out of the fuel) will cause a loss of flow rate. Therefore, a filter with a larger flow rate will be able to filter out more stuff than a smaller rated one before reducing flow to the point of fuel starvation.
That said, if you manage to pack up the filter, you've got other problems to address.
Hope this helps;