As others have already mentioned, at the very least, you want to separate out all SQL (or at least all the non-standard SQL) to some low level layer.

IMHO instead of writing this layer yourself, usually it's a good idea to use an ORM layer like DBIx::Class, which should also make many common database tasks much more convenient. Your own design will end up looking similar anyway.

In other words, you'll want to write as little SQL by hand as possible, and use whatever mechanism is convenient to handle the few DB specific variants (and ORM layers make that especially easy, since it's just a question of overriding the relevant methods).