I also got tired of leaving smudges on the screen, so I bought a cheap stylus that I use instead of my finger. Now I need to pull out my microfiber cloth 10x less often.
Regarding chapter management, there are a couple of things you can do. When you tap in the middle of the screen, you can open the reading menu, which shows a progress bar at the bottom, as well as the current page number. Tap the >| arrow on the right to jump to the start of the next chapter, and then look at the page number to see how far away it is. You can then tap on the handy "Back to page x" on the left side of the progress bar to return to where you were.
If you're reading a book with sub chapters, you can press and hold the page turn button to rapidly flip forwards a few pages to see if a new sub chapter is nearby, then hold the other page turn button to rapidly flip back to where you were. You can press and hold in the lower right and lower left corners of the screen to flip pages, too. Note that this only works in KEPUB books; if you sideload a regular EPUB, Kobo will display it using ADE, which lacks this feature (among others). It's generally worthwhile to convert all your books to KEPUB before you sideload them, which is one of the many things Calibre can do for you.