You're confusing design issues (how do I make a program that will deal with different databases and platforms) with packaging issues (MakeMaker and make). To answer your question, you have to decide whether these things can be changed on the fly (perhaps by user configuration) or whether you'll be producing specific versions for a given platform.

Conditional compilation a la C doesn't work too well in Perl, though there's a command-line switch that will run your code through a C preprocessor first. Instead, we generally use run-time conditionals. It is possible to make a module that provides a consistent interface to two or more different modules, so that clients don't have to concern themselves with cross-platform issues.

You probably will find it easier to stay in pure Perl and have a single version of your program that can run (possibly with different configuration) across multiple platforms. MakeMaker is more of a packaging tool.

Consider using object-oriented design for your system. If you have two different ways of doing something, make adapter classes (packages) with the same interface that do the something in each of the different ways. This way you can even mix the different ways (imagine having to deal with more than one different barcode scanner on a system at a time, or dealing with more than one database to allow copying and exporting).

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