Good rules for combining the various expansions start tiles
The details depend on which expansions you're playing with, as some have starting pieces that are mutually exclusive or have slightly different rules depending on the combination. For example, the following cover all expansions through the catapult:

Collect tiles:

Collect the following special tiles, in addition to those for the base game and any other expansions being played:


Any combination of river expansion tiles (from "The River", "The River II", or the "Mini Expansion") that includes exactly one spring, exactly one lake/end tile and, optionally a single branch and a second lake/end tile. 
The count piece and all 12 Carcassonne City tiles.


Prepare tiles:

Discard the starting tile; place the assembled City in the middle of the table, with the count in the castle district of the City; place the spring next to the City with the river leading away from the City, set one lake/end tile (with a volcano, if in use) and the branch tile aside, face up, and shuffle the remaining river expansion tiles and place them face down; shuffle all other tiles in use and place them in a concealed supply (in a bag, tower dispenser, or face down piles or stacks).

Drawing tiles:

Draw tiles, beginning with the branch tile, then face down river expansion tiles, then the face up lake/end tile, then from tiles in the supply.

For a step-by-step setup and turn structure tailored to whatever specific expansions you have in mind, see http://www.sciencegames.com/carcassonne/.