Well, now I can see where is the reason of the problem
Initially, the template had the container inside the slide, which initiated animation for the Scroll nav appear
So it was like this: when Container goes out of screen view, then Scroll nav appear.
When you start to adjust the template for yourself, you removed that container with text and so animation initiator does not exist, which means that Scroll nav do not appear anymore.
For fixing it, will be enough to connect any other element on your site to the animation "Show nav". I think slide or slider itself will be good enough (Slider moves out of the screen and Scroll nav will appear). So you just click on the slide (or pic whole slider element), go to "Objects" tab on the right side panel (with little cube icon) and click on the "Show nav" interaction.
Then, I noticed that on the template, they "turned off" the Scroll nav on the tablet and phone views. So if you will want to have that scroll nav, click on the Scroll nav element, then go to settings panel and click on the screen type, where you want to use Scroll nav.
Now about "cover image"
Here is again, it was that container, which has been creating the height of the slider (200 px of padding at the top and bottom).
Since now, you do not have this container, you will have to set height of slider element, or at least height of slide inside the slider. What this height should be is your decision: 500 px or 100%, or 200 px, whatever. Just do not forget to adjust it for every view: tablet, mobile-landscape, mobile-portrait.
Hope it helps.