The main difference is that SQLite is a much lighter engine that MySQL. This means that your application will have to do many more things that MySQL usually did for you. I'm in the process of converting one of my apps from Oracle to MySQL and while there's not a lot of changes, there's a few. (Primarily things like NVL() -> IFNULL() and the like.)

One thing we've considered is subclassing our database class. We have a class called ABCD::Database which provides business-level functions to the other classes. Sort of like canned queries. You could have an ABCD::Database::MySQL and an ABCD::Database::SQLite, which will seriously aid your migration.

The actual Perl you use will probably change very little, if at all. The changes will be in the SQL you use. (Unless, of course, you were using formatting functions in your SQL, in which case you may have to provide that functionality yourself.)