SMP/E includes ISPF panels which can be used to manage and track the installation of fixes, including constructing the necessary JCL.
IBM suggests that you do not apply maintenance to a running system. One consideration is that libraries under LLA control may not interact well with SMP/E. It is not a good idea to compress linklist libraries on the active system; if you run out of space while applying maintenance, then it can be difficult to continue. SMP/E ZAP processing includes an EXPAND function which invokes the linkage editor; however, ZAP will not see the relinked version of the module until LLA is refreshed.
See OE & SMP/E for considerations specific to the Unix System Services Environment and SMP/E Reports for information on extracting information from SMP/E.