Build the multifarm just like your normally would. I would recommend you put the platform on the top level, so the sugarcane grows above the multifarm, and you can get all your pipes in nice and easy.
Then, after you have built the platform, put the soil on top of the multifarm block material (for example, it should be on top of the stone bricks if that's the kind of multifarm you made).
If you want to use the Lilypad of Fertility, then leave a block missing in the middle of a group of the reeds and place the lilypad there (you need water for the lilypad to float on).