Not your time, other people's …
Despite the implicit oxymoron in the phrase, there is very little that a direct manager can do to directly manage, at least in terms of positive feedback. Of course in the longer term there is pay and bonus and opportunity for advancement, but within typical large corporations those are often more directly influenced by much higher levels of management, by personnel departments, by collective bargaining agreements and by other external influences. And there are softer factors; recognition and praise and general mentoring and guidance and leadership. But in terms of specific positive incentives, there is little that can be done during day-to-day operations.
However, in order to meet the flexible requirements of the flexible workplace, the least that a manager should do is show more flexibility. However junior her staff, she should allow them headroom and discretion. For example in a typical operation with an eight hour workday, there is no way that every day has exactly eight hours of work within it. There are some days when it is essential to do more than eight to meet immediate business deadlines. The obvious corollary is that there are times when it does not affect the business if particular staff work for less than eight.
Despite that, I'm not a believer in the old cliché of "she gets the job done, hours don't matter at all". That's wrong. Time counts too. Nobody can foresee and estimate everything required by "the job" in advance, so there is sometimes a requirement to just "be there". Contingency. Bums on seats. So the total should add up to (at least) those contracted. However a manager must be able to move hours, even if she is not permitted to create hours. It is impossible to manage normal business fluctuations without this discretion.