Magic Wand - Line Art

Adding to what Chuck has told you, you had the right idea using the Magic Wand, but instead of selecting each petal (using this flower as an example) make sure Contiguous is checked in the Options bar, and select outside the line art.

Then invert the selection (Shift Ctrl i — Shift Cmd i) and fill the selection with your colour of choice on a new layer below the line art layer.

Even if the line art is on a white background, you can make the white become transparent by changing the line art layer's blend mode to Multiply or Darken.

Or you can make an internal selection with the Magic Wand, and use Select > Modify > Expand to increas the selection by a couple of pixels, and fill that selection with colour as with the yellow.

Anotheer trick you can use is to Ctrl click a layer's thumbnail to load it as a selection, and then stroke the selection with black to create new line work around it.  If you do this using Layer Styles (double click the layer to open layer styles) then the stroke (as will all layer styles) is non destructive and can be edited.

Let's go back to the red petal layer.  Now you have that shape you can lock the transparent pixels as below

And apply gradients etc. and your line work remains unaffected.  To edit the gradient, double click it in the options bar.

I alsmot wish I was in your shoes starting out with Photoshop, because you have an exciting journey ahead of you.

Using magic wand directly sounds rather weird and unsophisticated, TBH. If it's really just line art, a simple Image --> Calculations to create  clean transparency would probably the better way. Then you can use that layer on top of everything and color in all the areas beneath using whatever method you prefer, including brushes or of course fills based on all manner of selections. Especially for small areas adding a bunch of basic brush strokes may be much more efficient then trying to get complex selections right...

Mylenium

I would have your line art on a separate layer. Then make sure you click in the empty space inside the lines. Then I would modify the selection by a pixel or two, depending on how thick you line art is. Then on a layer below the line art, I would fill with the color you want.