Is there a hardware user guide or some other documentation that I can download that details the recommended circuits for the BDM, reset pin, PLL, etc. for the S12X series? I need to know how to integrate this chip into a design using the recommended best practices. The datasheet doesn't really cover those important things in detail.
The most detailed documentation regarding MC9S12XA256 MCU you can find on page http://www.freescale.com/webapp/sps/site/prod_summary.jsp?code=S12XA& under Documentation Tab.
Please note that datasheet contains detailed specification of particular Part Numbers, more info you can find in Application Notes and Reference Manual describing details not covered in datasheet.
Most helpful info on hardware design you can find under Software & Tools tab (see section Evaluation/Development Boards and Systems). From there you can go to to description of boards (e.g. MC9S12XDP512 Evaluation Board) where is also published board schematics. Board description and schematics you can consider as recommended h/w application example. The EVB9S12XDP512 User's Manual is posted under Documentation Tab.
As general, but also useful you can find on-line training Effective Printed Circuit Board Design (http://www.freescale.com/webapp/sps/site/training_information.jsp?code=WBNR_PCBDESIGN ).
There is an Application Note exactly for this purpose, the AN3262 Designing Hardware for the MC9S12XD family:
The guidelines can be used for designing with S12XA family as well.