BPM 12c has been the latest released version for almost two years now. BPM 11g installations should be looking at 12c upgrades to either pick up significant new features in 12c or prepare for 11g end of support. The upgrade can be quite involved depending on how complex the existing 11g environment is and how much running, faulted and completed instance data it contains. In all but the most trivial cases it will require careful planning and testing.
A caveat to be aware of is that 12.1.3.x, the initial 12c release support dates are based on WebLogic 12.1.x which came out a couple years before BPM 12.1.3. The end of support for WebLogic/BPM 12.1.3 is the December 2017, a year earlier than BPM 11g PS6 BP8 (220.127.116.11.8). If your upgrade planning is driven by support considerations 12c R2 (12.2.1.x) is a better target than 12c R1 (12.1.3.x).
(n.b. find a better table or graphic for below info)
There are major differences in BPM 12c. Some of the headliners are WebLogic 12.x vs. 10.3.6, new internal data model for instance data, BAM completely rewritten and cluster capable, Oracle Enterprise Manager/Fusion Middleware Control UI new and improved (even more so in 12.21 than 12.1.3). The cleanest and least problematic upgrade will be to build new 12c infrastructure, convert BPM Studio projects, redeploy and cut over or phase over. It is possible to do an in-place upgrade if cut over operations is not an option. Instance data will be restructured, WebLogic domains will be reconfigured, BPM Composer projects will be converted and transferred from PML to PAM. Deployed composites will continue to work as-is, the BPM run-time will dynamically convert deployed 11g composites to 12c every time they are loaded in memory. If you have a lot of instance data in various states with multiple composites involved in a flow it may be difficult to do a before-after accounting of the data. If you are using partitions for your 11g instance data, in-place upgrade is only possible with 12.2.1 not 12.1.3.
In short, R2 (12.2.1) is behind R1 (12.1.3) in bug fixes for engine function and performance and BPM Composer/PAM function. R1 has BP6 available April 2016 which address those bugs while R2 does not have its first BP until June 2016. If you must do the upgrade before July 2016 then R1 is the only real option. If you have partitioned instance data then you will need to build R1 new and cut over as mentioned above. Generally it will likely be best to wait for R2 to catch up with fixes in BP1 coming out in June.
BPM 11g PS5 (18.104.22.168) is the lowest supported starting point for in-place upgrade. Even though, if possible move to PS6 (22.214.171.124) first. In either case, apply the latest bundle patch - BP7 for PS5 (126.96.36.199.7) and BP8 for PS6 (188.8.131.52.8). Make sure the 11g installation and instance data are clean and healthy, purge or archive as much instance data as possible. ldentify any 11g deployed composites missing source that will not be able to be converted and redeployed.
If you have BAM in the same domain as BPM you will need to do a hybrid in-place/cut over upgrade. BAM servers will need to be split out to a separate domain removing them from the BPM domain. The BPM domain can then be upgrade in-place while the BAM domain is built new and cut over.
If EM is being used for operations and monitoring it is important to learn the differences in flow structure and audit trace and train operations staff appropriately. The Middleware Control part of EM is significantly changed from 11g to 12.1.3 and the UI significantly changed again from 12.1.3 to 12.2.1. If using instance name (via ora:setCompositeInstanceTitle() or otherwise) to search instance data it will not be obvious how to do a similar search in 12c EM.
The most import part of running an upgrade is to do a test upgrade on clone of your production environment or as like production as possible. UAT or pre-production are good candidates if you can get representative instance data loaded from production. The second most important thing is to have a complete and proven backup of production before doing the upgrade.