Hi Lemonmomma, and welcome to garden.org
It's fine to fertilize when there are flowers on your lemon, BUT:
We need more info to advise you if you should - how long ago did you pot up your little lemon? Since you used 1/4 manure in your potting mix, there still may be some residual manure feeding the tree. That's a problem with using manures - you really don't know how much nutrient value they have or how long it will last. Adding more fertilizer on top of a high dose of nitrogen from the manure could give you burnt leaves.
It will also help us to know where you are on the planet - if you could fill in your profile with your location, please. This determines how warm it's been all summer IF your lemon is growing outdoors?? How much you've been watering it, and how much rain it's had will help to guess if the manure has exhausted it's nutrients yet. If you are in Florida for example, then it's definitely ok to give a light dose of fertilizer in the fall but somewhere further north, where the plant is going to slow down due to lower light levels and cooler temperatures (or indoor conditions if you take it indoors in winter) might mean you should wait.
How big is your plant and how big is the pot? A picture will be very helpful here. A very small baby lemon tree will need light fertilizer, and you should not let it set any fruit for its first year. (I know, that's tough to hear but . . it needs to make more roots and leaves to support making fruit next year and in future)