Left mouse button is the drag tool. It moves and accelerates all particles within a certain radius from the mouse pointer. The radius can be changed by pressing F2. Note that the effect of the tool fades out as the distance from the mouse increases. This allows large jellies to be dragged without damaging them - but it also means that a small jelly may still be damaged if you drag it too fast.
Right mouse button is the rotate tool. It uses the same radius setting as the drag tool. This tool may be a bit confusing because it is only applied when the mouse moves. Hence, to spin an object you need to hold the RMB and move the mouse back and forth slightly.
Shift+drag, Ctrl+drag and Alt+drag modify the strength of the tool. The weakest spin is applied with Shift held down, then comes Ctrl, then no key, and Alt produces the strongest effect.
Press S to pause and resume simulation. Note that tools seem to do nothing when the simulation is paused, but in fact their effect accumulates until you resume simulation.
Press Q to enter or leave the Quick Edit mode. This mode makes it much easier to set up a specific position of the jelly because gravity is turned off and all movement stops fast. When you leave the mode, the previous values for gravity and damping are restored.
If you want to set up a complex scenario, use the E and R keys. The E key will save the scene into a file called (snapshot).jel, and the R key will load it. Once you're happy with your scenario, you can save it into a separate file. The R key simply reloads the file that you last dealt with, so you can also use it to restart a file that you loaded last.