In between levels, you can upgrade various attributes of each tower to make them more powerful, fire faster, and decrease training time for deployable units. As an extra line of defense you also have three special abilities you can upgrade (that you'll unlock as you play) for when the towers are not quite enough. You can deploy units on the ground to back up your knights or you have a "nuking" ability for emergencies (like a flaming meteor). Both have a cool-down time (more so for the nuke ability) so you'll need to pick the best time to use them. Your third instant special ability is yours to choose, by buying items in the in-game store. Each stage you'll earn a number of gems that can be used to purchase items in between stages. I've had some luck using an ability that lets you drop a potion to freeze enemies for a short time, but, if you have the gems, there's even a "Fat Boy" nuclear weapon that clears the map.
Another cool element of the game is the ability to use and upgrade a hero: a single named unit with special abilities that you can direct to any area of the battlefield. The hero comes in handy in particularly difficult battles, and you'll have three different types that unlock as you play. Kingdom Rush Frontiers (like the original) also has several heroes you can unlock for as much as $7.99 in real money, but the three you get simply from playing are quite powerful on their own.
There are some new towers you can unlock once you get into the fourth tier that have upgrades to let you focus on specific abilities. The Archer Tower, for example, lets you upgrade to a Crossbow Fort. From there you can choose from two abilities, including one that increases range and another that shoots a barrage of powerful arrows. Each game you start fresh at the lowest tier, so upgrading the correct towers to the highest level is part of a winning strategy.
Like many games these days, you also can buy more gems with real money, but I found I can do just fine without ponying up any extra cash. Even when a level seems like it can't be beat, you usually only need to rethink your strategy, so think twice before deciding to spend any real cash.