It would be best to plan nice topology from the beginning. You can form the 'pill' shape with a circle, splitting(Y) it's half, moving it and filling everything(F), if you then inset(i) the resulting face, you get the geometry that you can use to re-form a circle by snapping half of it back to place(hold Ctrl down while in transform operation to temporarily enable snapping, be sure to use vertex snapping). You need to merge the overlapping vertices with merge by distance(Alt+M) and then you can extrude your hole.

There are obviously plenty of other ways to do this and none of them is 'the right one', my main point is that it is best to plan from the start while modelling and have nice topology. You will find it a lot more convenient than using booleans and having a mess in the long run. If this seems a bit overwhelming, because you are just beginning don't worry too much, just keep in mind that planning and keeping in mind what other operations you are going to need while modelling is a good idea. You need to get used to all the modelling functions in order to put all the pieces together in your mind for a specific shape.