I'd avoid auto-dimensioning, that may work OK, but it depends greatly on how you made the model in the first place. You'd probably spend more time tweaking the result than its worth.
You can either use standard dimensions (extension lines and an arrow at each end) or Ordinate dimensions where you pick a 0,0 and all dimensions are a single extension line + number based off that zero.
Ordinate if far less clutter, but often having a single 0,0 is not the best for manufacturing so a machinist may have to use a calculator to back-calculate some features at the far end.
A quick googleyields:http://www.maelabs.ucsd.edu/mae_guides/CAD/Dimensioning/Dimensioning_Fundementals.htm
Sheet metal works exceptionally well with Ordinate dimensions, and milled parts such as when using a Digital Readout.
I find most lathe parts have features at both ends (remove part from collet machine the other end) so I like dimensions "from each end"
I'd say it depends on your method of machining. To make your machinist happy, dimension it like you would machine it.
To make it easier to QC, use ordinate and make the 0,0 a useful feature you can repeatly fixture off of.
The latest methods go further than just the: "Geometric Design and Tolerances" GD&T. This method improves yield by allowing more realistic tolerance zones. Some call it something like tolerance of position.http://en.wikipedia.org/wiki/Geometric_dimensioning_and_tolerancing
For homemade items, low volume, or non precision parts its not necessary, but for production it a money/material saver.