QUOTE: “Medium pages achieve their purpose and have neither high nor low expertise, authoritativeness, and trustworthiness. However, Medium pages lack the characteristics that would support a higher quality rating. Occasionally, you will find a page with a mix of high and low quality characteristics. In those cases, the best page quality rating may be Medium.” Google Quality Evaluator Guidelines, 2017

I do not obsess about site architecture as much as I used to…. but I always ensure my pages I want to be indexed are all available from a crawl from the home page – and I still emphasise important pages by linking to them where relevant. I always aim to get THE most important exact match anchor text pointing to the page from internal links – but I avoid abusing internals and avoid overtly manipulative internal links that are not grammatically correct, for instance..
The Java program is fairly intuitive, with easy-to-navigate tabs. Additionally, you can export any or all of the data into Excel for further analysis. So say you're using Optify, Moz, or RavenSEO to monitor your links or rankings for specific keywords -- you could simply create a .csv file from your spreadsheet, make a few adjustments for the proper formatting, and upload it to those tools.