Building Custom Index.php

I have been searching the forum for an answer and maybe I am not asking the question correctly so, have two related questions: I’m building my first theme from HTML and CSS and have read the codex but I am still unclear of the correct process for building a custom home page that pulls multiple posts into magazine layout style home page that will display featured, recent and then category specific rows of content. I don’t need any dashboard configuration since it just needs to be hard wired in for my own use. Can I just alter the index.php to display the home page the way I want it?

I have created custom home pages for static front page themes before but this is different and I am unsure of the correct process and noobie with php.

Second, any direction to examples of the code to get posts to display a magazine layout (similar to this: http://www.lovemeagan.com) to match what I have created in my HTML would be very much appreciated. I am building from scratch and appreciate any assistance. I can deconstruct visually but php documentation is still overwhelming and just confusing me. Thank you for your help!