Running w/ boots is harder for two reasons: 1. They're not soft and cushy like running shoes. 2. They're just plain heavier. LOTS heavier than running shoes.
I swear by Sof Run+ insoles. They'll run you about $15-20 a set, but man are the comfy. Saved me at Parris Island, and at TBS, too.
Speaking of TBS, if ever there were a time that you'll get very, VERY used to running in boots and utes, that's it. I can think of maybe four times in six months when we wore just plain PT gear. And since my SPC was all about "Medieval PT", we wore boots, utes, and a minimum of a flak, but generally he added helmets/patrol pack/rifles, too. And we always, always, ALWAYS went swimming...On every run.
Ah... Such simpler times. No EPs, no limits, no RIs. Just lots of err's, yut's, oorah's, sweat, etc.