You don't need to do anything special with Apache, you just need to use the correct interface in PHP. That is, the mssql stuff that Tobias linked to, or - perhaps better - PDO which can be configured to use either MySQL or MS SQL. PDO would probably be a lot easier going forward if you have to end up supporting both database engines.
In terms of differences between the MySQL and SQL Server, there are quite a lot unfortunately. Most annoying will be that the syntax for certain types of queries will be slightly different (and DDL - that is, creating tables, indexes and so on - is completely different!) Though they both support a big enough subset of standard SQL that you can usually find a way to do most everything that works in both of them. But don't expect to just connect to SQL Server and have all of your queries written for MySQL "just work" - unfortunately, they won't.
I guess in the end, the easiest thing to do is just to try it out. If it looks like it's going to be too much (for example, if you're using a lot of 'obscure' MySQL features), then you might have to rethink your options.