I am working quite a lot now with Keynote 6 and LaTeXiT, and find two sorts of work flow convenient:
(1) Put a brand new formula on your slide
(1.1) Format formula with LaTeXiT
(1.2) Drag and drop pdf formula from uper window of LaTeXiT onto some suitable directory in finder.
This creates a pdf file containing the formatted formula
(1.3) Drag and drop the pdf file with formula from finder to Keynote slide
(1.4) Re-position formula with Format --> Arrange ---> Position in Keynote if neccessary
(2) Modify and existing formula on your slide
(2.1) Now you should have a formula pdf file in some directory, as sketched in (1)
(2.2) Drag and drop formula file from finder directory to upper window of LaTeXiT.
(2.3) Modify and re-format formula with LaTeXiT
(2.4) Drag and drop the formula into finder directory
(2.5) Mark old formula on slide
(2.6) Use Format --> Image --> Replace in Keynote, select new formula in file selection menu
(2.7) In several cases, the new formula will not fit properly on the slide.
Then press Format -> Arrange -> Original Size. This should display the picture properly, and you can
re-size it according to your needs