I have a DB that is locking up from numerous updates to a table: Should I convert it from MyISAM to InnoDB?
In almost every use case, InnoDB is preferred over MyISAM.  So, yes.

To make sure the indexes, etc are converted correctly, see if anything in MySQL to InnoDB checklist needs to be addressed.  Note that key_buffer_size should be decreased and innodb_buffer_pool_size increased.

In MyISAM, an UPDATE blocks all other operations on the table.  In InnoDB, it blocks only the one row (assuming the WHERE clause restricts the scope to a single row).

It is ok to have a mixture of MyISAM tables and InnoDB tables.