The FL Studio 9.9 Beta introduces the 'Patcher' plugin. In this video the Guru runs though some basic operational principles. Patcher will load as an Instrument Channel or Effect and from there you can happily chain both instrument and effects plugins.
Use Patcher to create and save your favorite instrument & effects chains
For more information visit Looptalk to see how to add 3rd party VST's to Chainer.
EDIT: The first Patcher Tutorial is here.