Summarising ChIP-seq and controls needed
Good experiment! ChIP-seq is good for a whole genome look at transcription factor binding. KEY POINT:  The data generated are only as good as the antibody. Considerable effort needs to taken to prove antibody is specific for only the protein of interest.  It is for this reason, that some TFs still haven't been characterized by ChIP-seq.

As far as controls for your experiment:

The breaking of DNA from sonication isn't uniform from experiment to experiment, and sonication will preferentially break at some regions of open chromatin more often.
Controls for this:


Isolate DNA from cells that have been x-linked and fragmented under same conditions but don't use antibodies to IP.  This is "Input" DNA.
You can conduct a "mock" ChIP using a control AB that reacts with some non important non-nuclear protein, such as IgG.  


Then sequence these samples to same depth as the Immunoprecipitated DNA.

Here is a good paper that is a little dated, but still relevent: Go to Control Sample Section

Here is a link to the guidelines for ChIP-seq for ENCODE PDF

Last but not least, if you are working on a much smaller scale, don't forget about things like DNA footprinting and EMSA to identify the ACTUAL binding site.