A lot of the answer to you question will depend on what kind of surface style you intend to write in. I don't think you can really seperate deep-level structure from what happens 'on top' of the music. Some composers deliberately choose a style in which the sections, be that a melody, a chord, a texture, are very clear (Poulenc, mid-baroque, some minimalists, film scores) whereas at the opposite extreme some write their music as what seems like an endless transition from start to finish (Wagner, Sibelius, contemporary spectralist and other schools of minimalism). So the terms of what constitutes 'logical' structure and development will depend on what your long-range goal of the piece is. As you seem to be just starting out learning to compose, I would guess that you're probably experimenting more with the former style, which is fine. You might want to plan out different sections for a piece based on forms you've already encountered (things like minuet and trio movements or variations) and then come up with related ideas for the surface material, which you can then work out what goes where.
You could alternatively take a single idea or process and follow it through. Some good examples of this appear in contemporary music, such as Arvo Pärt's Cantus in Memorium Benjamin Britten, which uses just a descending scale played at different speeds in the string orchestra. Or the minimalist works by Steve Reich and others where two versions of the same thing are played with one slightly faster than the other and the piece ends when they coincide again. A simple canon is another example of this.