Two instances better - or mix MyISAM and InnoDB?

I may have submitted this question to the wrong forum. I'll try here.

We use MySQL to support a large OLAP type application with one very large table that is only updated once a month. By large, I mean 1.5 billion rows. We use MyISAM for this table for performance reasons, and also because we use merge tables to facilitate the monthly updates (dropping the oldest merge table, and adding a new one).

We are developing a new application that is highly relational and makes heavy use of real-time user-driven transactions with joins and commits. We will be using Innodb tables for this functionality.

We have a dedicated db server that currently runs one instance of MySQL with the MyISAM table format. To support the new transaction-driven functionality under development is it better to continue with one instance of MySQL and mix the two table types, or would it be better to run two instances of MySQL, with different ports and data directories?

Thank you for any insight you might have...

-Jim Gallagher