To elaborate on what "don_3259" wrote...
The "unwrap_uv" modifier allows you unwrap your mesh multiple times using different "Map Channels".
By default this is set to "1" however if you change this to "2" it will prompt you to MOVE your UV information to Map Channel 2 or ABANDON which means start afresh. Next to this option there is also a SAVE and LOAD - this allows you to save your UV information to a .UVW file and load it again when needed. Now your model is probably unwrapped nicely but when you view this in the Unwrap Editor it's all overlapping because it's linked to more than 1 texture map. You probably want to retain this but as said you want to combine it to a single texture file such as JPG.
Here are the steps:
[Setting up the UV's]
01. In the Unwrap UV click SAVE to save your current UV information to a .UVW file
02. Set the MAP CHANNEL = 2 and select ABANDON
-- this allows you to unwrap your mesh completely differently without affecting how it has been unwrapped on MAP CHANNEL 1
03. Click LOAD and load your .UVW file
-- this has basically setup MAP CHANNEL 2 to be exactly the same as MAP CHANNEL 1
04. Open the Unwrap Editor and Pack UV's : Tools > Pack UV's
-- this will basically keep how everything has been unwrapped but position it all side-by-side so there is no overlapping
-- you can also do this step manually if preferred
05. Click SAVE to create a second .UVW file of this second MAP CHANNEL 2
[Baking a new texture]
By this point your model has been unwrapped 2 different ways MAP CHANNEL 1 = Original and MAP CHANNEL 2 = laid out for a single texture file.
06. Select your model and open the "Render to Texture" window : Rendering > Render To Texture
07. Under "Mapping Coordinates" select "Use Existing Channel" and select CHANNEL 2 from the drop-down
08. Click ADD and select DiffuseMap - set your desired output path, filetype (eg. JPG) and resolution eg. 2048 x 2048
09. Click Render and it will create this file
[Assigning the new Texture]
The following steps removes the new MAP CHANNEL 2 and you use LOAD UVW to load which layout you want to use.
10. Add the modifier "UVW Mapping Clear" and set this to 2
-- this will remove the MAP CHANNEL 2
11. Collapse the stack and re-add the "Unwrap UVW" modifier
12. Click LOAD and select the second UVW file you saved
13. Assign the new texture file you just baked and done!
There are a lot of steps - let me know if you get stuck with any section.