Try to rough out a touring schedule first, keeping in mind which parks have EMH and when. (For example, my family tries to avoid the parks with EMH because they tend to have a slightly larger crowd, unless we're there during a high-traffic time like Easter or Christmas, when using EMH is more of a necessity. but we always start and end with MK regardless. If we do make use of morning EMH at one park, then in the afternoon after our naptime we hop to a park that has no EMH that day. We never keep the kids up late for evening EMH, but we avoid the park that has them when we decide where we're going on a particular evening.)
Once you have an idea of what your "evening" park will be every day, I would suggest making all of your FP+ there. (Obviously, if you have dinner reservations anywhere, this will answer that question for you!) If you arrive at your morning park at rope drop and hit the headliners first, you won't need your FP+ in the morning. (Of course, if you're taking an evening "off" to swim or see a dinner show -- we often do this on our HS day, because we can't fill a whole day there -- then by all means use your FP+ in your morning park).
FP+ has changed our touring plans in one sort of significant way: we used to make several evening "hops" to Epcot for dinner reservations. However, Epcot FP+ are tiered in such a way that you only get one FP+ of any value. Now we're more likely to visit Epcot over two mornings (one where we head to TT first and one where we head to Soarin' first), and hop to the MK on those days, where there are far more FP+-worthy attractions, and no restrictions on how to use our 3-FP+ allotment. This means fewer dinners in Epcot, but more chances to explore TS dinner venues in the MK and at the monorail resorts.
Good luck!
(If it helps, this is how my family has typically scheduled our trip with small children -- I added FP+ where we used to use the legacy FP -- and it worked well). For anything that my then-4-year-old was too small (or too scared) to ride, my DH just took her to a nearby M&G or a more benign attraction. (e.g., Pirate's Adventure scavenger hunt in Adventureland instead of Splash Mountain, Tomorrowland Speedway instead of Space Mountain, Triceratop Spin instead of Expedition Everest...)
Day 1 - Travel/MK (Adventureland, Frontierland, Liberty Square, w/FP+ for Splash, Big Thunder, Jungle Cruise)
Day 2 - HS (FP+ or rope drop for TSMM, RnR, ToT, Star Tours) / Naps / Hoop-de-Doo Revue or another special dinner outside of a park
Day 3 - AK (whole park, rope drop for Kilimanjaro Safaris and Expedition Everest) / Naps / Epcot (Future World, FP+ for Soarin')
Day 4 - Epcot (rope drop for Test Track, Character Spot, Sum of All Thrills, then proceed to World Showcase) / MK (Tomorrowland and New Fantasyland, w/FP+ for Space Mountain, Buzz Lightyear, Enchanted Tales w/Belle)
Day 5 - HS (rope drop for Jedi Training Academy, then see the shows missed on Day 2) / Naps / MK (finish Fantasyland, FP+ for Princess Fairytale Hall, Peter Pan, Pooh)
Day 6 - revisit MK for favorite attractions before departing (FP+ for Splash Mountain, Big Thunder Mountain, Peter Pan)