The easiest way to install RetopoFlow is to do so directly from Blender. You can do this by going to File > User Preferences > Add-ons > Install from File. This will open a File Browser in Blender, allowing to you navigate to and select the .zip file you downloaded. Press Install from file.
Once activated, a new Retopology panel will be added to the viewport toolbar, so long as a mesh object is selected. The toolbar is shown in both Object Mode and Edit Mode under the Retopology tab.
To use any of the RetopoFlow tools you must first select the model you wish to retopologize. RetopoFlow will create the new geometry based on the surface of this existing model. For the time being you may only select one object to retopologize.
After an object is selected, in Object Mode, simply press the Contours or Polystrips button from the 3D view toolbar. Each of these buttons will activate their respective modal operator, meaning you'll be placed into an interactive tool until you confirm or cancel the action (exactly like Blender's default knife tool). You may also activate Contours or Polystrips from a menu with the hotkey of ctrl + shift + V.
While the RetopoFlow tool modals are active you can open the help panel anytime by clicking on it with your left mouse button. Close it by clicking anywhere on the panel.
The help panel is a great way to quickly learn how to use RetopoFlow or for reference specific options.
Draw strokes - LMB
Once activated you can draw strokes with your LMB across cylindrical forms to generate loops for the retopology mesh. These generated loops will automatically conform to the underlying surface (as designated by the selected object).
Adjust segments - shift + wheel
You can increase/decrease the number of segments in the contoured segment with your mouse's scroll wheel.
The mouse button used for selection is as defined by your chosen button in User Preferences > Input > Mouse > Select With. Blender default is the right mouse button.
To slide a stroke along the form just select it and press the G key.
Rotate stroke - R
With a stroke selected you can rotate it with the R key.
Shift loop verts - Left / Right arrows
While a stroke is selected you can shift it's vertices around the form with the left and right arrow keys.
Delete stroke - X
You may delete a selected stroke with the X key.
Toggle Guide Mode - TAB
You may enter guide mode, used for generating multiple strokes at one time, by pressing the TAB key. Once in guide mode you may draw a path along a cylindrical form to create strokes over the full length. If previous strokes exist then you can extend from those strokes by first hovering over an open end.
Exit guide mode with TAB again.
Draw strips - LMB
While Polystrips is active you may draw new strips by Left-Click-and-Dragging across the surface of the mesh. Start drawing from or onto an existing strip/junction to snap the new strip to the existing.
Strips, junctions, and handles may be selected with the selection mouse, as set in your User Preferences.
Rotate strip/junction - R
With a strip or junction selected you can rotate it with the R key.
Scale strip/junction - S
Strips and junctions (endpoints) can be scaled with the S key when selected. Adjusting the scale will dynamically set the segment count of the strip to fit.
Knife cut - K
If you need to add additional junctions into an existing strip, simply hover your mouse where you'd like the junction and press the K key to cut in a new junction.
Merge junctions - M
With a junction selected you may merge it into another junction by hovering your mouse over the second junction (to be merged into) and press the M key..
Delete strip/junction - X
The selected strip/junction can be deleted with the X key.
Dissolve junction - CTRL + D
Use CTRL+D to dissolve the selected junction from it's parent strip. Note, this only works if the junction is relied upon by other strips (such as a T-connection).
Adjust strip segments - shift + wheel
With a strip selected you may adjust the number of polygons in the strip. Doing this will lock the strip, such that additional transform will no longer dynamically adjust the segment count.
Change junction type - CTRL + C
Junction types for the selected junction can be changed with CTRL+C. Press CTRL+C repetitiously to cycle through junction types.
Patch filling - shift + F
You can fill the area between selected strips in order to complete the mesh.
Supported patch types (as defined by number of strips) are 3, 4, and 5 sided patches. Each junction in the patch must be an L-type junction.
Tweak mode - hold T + draw with LMB
At anytime during the Polystrips modal you may tweak individual vertex positions. Doing this will lock the strip/patch the vertex belongs to, meaning it'll no longer be dynamic.
If you're working in Edit Mode then you may also tweak existing geometry in the active mesh.