Are you trying to encourage more growth? Fertilise in spring and early summer with a balanced fertiliser.

Compensate for a particular soil problem? Probably at any time including now.

Encourage flowering? Don't randomly throw fertiliser at it. If there is a particular problem, identify it and then apply the correct fertiliser. Incorrect fertiliser may reduce flowering or even harm the tree.

Well-rotted manure can be applied at any time. Make sure it is well-rotted, Magnolias won't thank you for using the fresh stuff.

Magnolias don't need ericaceous soil, they grow fine in neutral or even slightly alkaline soil, as well as the recommended slightly acid soil. Unless you have moderately or very alkaline soil (lots of chalk or limestone), you shouldn't need to worry about this.

You can pop some of the manure on top now if you like, but plan on using some fertiliser next year. Its hard to maintain a good eco-system in a pot that would fertilise "naturally" simply by adding organic material. You can use a time-release fertiliser mixed into the soil every spring, or a soluble fertiliser when you water, whichever you prefer. You can use an ericaceous fertiliser but don't use the ones that have a big nitrogen number. Pick one with all three numbers about equal.