How to architect a Java Enterprise application?

I am given a task of Revamping a Commodity Sourcing project written by previous programmers.

The problem is the old guys didn't follow any Rules of Software Architecture, OOP or simple Naming convention. E.G

1-Single POJO is defined which serves both as Session bean and entity bean, which lead to a complex structure and duplicate code everywhere.

2-There is no N-Tier Architecture followed, which leads to almost unreadable code and over 5K lines of code in one class.

3-No Design Patterns of any sorts is practiced

Currently, we AngularJS is used on Front-End, and SparkJava(Not Apache Spark) in the Back-End. Following is what is Current Architecture (sort of)

I know very Basic

Since I have to start from the ground up. Can Anyone refer to a good resource on how I can design application that follows strict architecture rules and conventions.