1) I would read all the Help files
2) Make small files of only one family and practice.
3) Look to see how many individuals in common the two files might have. Consider splitting files so as to merge as few people as possible with each merge. You don't want to be merging two files that have 1,000 people in common.
Since you are merging a mom's side and dad's side, you shouldn't have too many people in commnon. Do you have any cousin marriages above the parents that make them related to each other? I would consider disconnecting cousin marriages, or make note of them and look at them after the merge to see that cousin marriages didn't end up with duplicate spouses from different trees.