FIX patch: A patch that corrects sequence or reduces an assembly gap in a given major release. FIX patch sequences are meant to be incorporated into the primary or existing alt-loci assembly units at the next major release, and their accessions will then be deprecated.
To me, patches are just for a historical record, but not intended for practical use. If you integrate them into the primary assembly, all the coordinates will be shifted. Then your results cannot be easily compared to others. If you treat them as separate contigs, the massive redundancy with the primary assembly will lead to loss of information around patches, which is also problematic.
If you are worrying about the misassemblies in the reference genome messing up your analysis, you should really use decoy sequences.
Currently, it is challenging to use the patches. Tools are being developed to make better use of the data, but they are not quite ready for prime time. Jeremy and JC are correct- you can integrate the sequences into the assembly using the information the GRC distributes but you will create chromosome coordinates that don't exist anywhere beyond your computer. However, if this is just an analysis intermediate and you map features back to the native (that is scaffold) coordinates then you would be fine.
Note: there are two types of patches- the FIX patches are regions where there is a mis-assembly and the Primary assembly (i.e. the chromosome assembly) will change when GRCh38 is released next year. The NOVEL patches actually represent places where the underlying chromosome assembly seems to be correct, but an additionally allele that adds more sequence has been found.
There is an aligner that can use the assembly structure (that is the placement file that provides the correspondance of the patches/alts to the assembly) and provide alignments that don't get a lower mapping score: ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/srprism
This aligner is not published yet, but a manuscript is in preparation.
Patches are not normally intended to be applied to the primary sequence, otherwise the GRC would have provided tools to easily do so. You can certainly include the patch sequences in your genomic index for the purposes of alignment, but you will be working off the grid, so to speak.