Yes, it may sound as if you're over-enunciating or speaking exaggeratedly clearly, but comprehension will not be a problem. When we Swedes slow down we tend to do this as well (saying är instead of e or och instead of å, for example).
Note that this doesn't apply to letter combinations that are always to form a combined and distinct sound, such as the sj-sounds (skjorta, sked, charmig statiom, stjärna, for example) or the various spellings of j (hjul, ljus, etc.). Those should never be pronounced as individual letters but always the sound they represent. You would still be understood, but it would sound rather strange.
Depending on your operating system, you may be able to change your keyboard setting to the "English International" keyboard, which will allow you to type the accented letters using shortcuts. If you don't want to change your keyboard setting, there are buttons underneath the text input box on the Duolingo interface that you can click on to input the Swedish characters. Don't hesitate to reply to this comment with any further questions about either route.