Hi there - I'm a certified Google Partner and manage about $60k in spend a month.
I would first of all not use custom UTM tracking URLs for AdWords. Since Google AdWords and Analytics are tightly integrated, go with the default tracking and see what your data looks like.
If you are still not seeing the data you'd expect, next take a look at your conversion path. For instance, if you are running an ecommerce site, and you hop from www.mysite.com to store.mysite.com, there may be a break there. Another common issue is using a third-party gateway, i.e. www.mysite.com > PayPal > www.mysite.com/confirmation-page (which can be resolved using the admin feature: Referral Exclusion List).
Another thing to look at is Google Analytics > Landing Pages. You can pull up one of your AdWords-fueled landing pages, and a secondary dimension of Source/Medium to see if in fact you are correctly tracking AdWords to that page. If that traffic seems to disappear on your site, and otherwise possibly end up as Direct, then the disconnect is on your site, not in the UTM tracking parameters.
Regarding Direct traffic, you can generally expect that about half of it is unattributed organic search (depending on where your traffic normally comes from). The balance of is it direct traffic, bookmarks and some amount of unattributed (for whatever reason) traffic. I would not group Direct with your Paid Traffic spend in order to calculate ROAS.
Regarding your last question, if your traffic is coming directly from AdWords, then conversions should be attributed to AdWords. You can also take a look at your multi-channel attribution to see if AdWords contributed to any purchases with a different 'last-touch' attribution.
Bottom line is that you have to get your tracking tightened up, and not make assumptions about Direct traffic. Start by going with default UTM tracking on AdWords, and don't create custom UTM tracking URLs. See how your data looks from there (both at the landing page level and through conversions) and that should help identify where things are breaking down. From there you can move on to how you're tracking your other channels, be they paid or organic.
Hope this helps and good luck!
