When my suite was fitted the plumber ensured he left a gap behind the cistern etc for the tiler who would be coming later, therefore I believe you fit the suite, then tile around it.
As for the floor covering, you mention tiles. If it is an upstairs bathroom this is a bad idea as the flexibility in the floor will result in the tiles coming loose very quickly, therefore I used the vinyl stick down type. If it is a downstairs bathroom you're OK to use ceramic ones.