Using the flower to rejuve stamina is silly; please don't do that. You can also use it to increase your harem and accessory limit, and it'll take hundreds of them to get the girls you want from premium gacha unless you have supreme luck, so even if you buy nutaku gold you probably want to use flowers sparingly.

Best ways to get manyu: I recommend going for 3* in all normal missions from bottom to top, making sure you have enough stamina to get the bonus missions when they appear. Focus on using manyu on the 20 girls you want in your team, but once they're 24 or so the weakest manyu doesn't help them much, so you can use it on other girls instead, and after 40 or so the midlevel manyu isn't as effective.

Oh, and it's generally better to do higher level missions rather than lower level missions as long as you've already gotten 3* on the missions. Some will say it's more worth-while to do the lower level quests, but it's a waste of time to get those weak raid-bosses and you have chances at better rewards from chests in chapter 12... and at least a chance at much better manyu quality from the bonus stages.