This depends. Epilepsy and clinical neurophysiology fellowships aren't competitive (save for really, really desirable places). As a rule, pretty much ALL of the fellowships in neurology are noncompetitive. Headache, neuromuscular, movement disorders, neuro-onc, neurocritical care etc. Possible exceptions include neurointerventional, pain medicine, and sleep medicine.
So my first advice is to relax if you're interested in epilepsy or CNP.
A great time to start thinking about choice of fellowship is in the ending phases of PGY-2 year. You need to start building a schedule for your PGY-3 year that will expose you to various fellowship interests to confirm/refute you thoughts and experiences at the end of PGY-2. You will be submitting applications at the end of your PGY-3 year and beginning of your PGY-4 year.
By late in the PGY-3 year, you should have mapped out a set of programs you want to interview at and have your mentors working on letters of recommendation. You should also be double-checking your own PGY-4 schedule to figure out when you can or cannot go on interviews (depending on how stringent your home program is about taking interview/vacation days as a senior).
You should have few to zero problems. Don't worry and good luck.