System Architect is used to build architectures using various frameworks including TOGAF, ArchiMate, DoDAF, MODAF, NAF and standard method notations such as sysML, UML, BPMN, and relational data modeling.

Most simply, users use EA and System Architect to build diagrammatic and textual models of any and all aspects of their organization, including the who, what, where, when, why, and how things are done so they can understand the current situation, and plan for the future.

The Architecture Development and Analysis Survey, conducted by MITRE Corporation for the US Office of the Assistant Secretary of Defense for Networks & Information Integration (OASD NII) and revealed at the CISA worldwide conference on December 1, 2005, reported that out of 96 programs building DoDAF architectures responding to the survey, 77% used System Architect, either by itself (48%) or in conjunction with another modeling tool (29%).

This is termed in the industry as 'data centric' behavior, which forms the core tenet of Model Based Systems Engineering (MBSE).

Users may also work in a stand-alone configuration on their laptop or workstation using SQL Server Express, which is bundled with the product.

Users may customize this meta model, to change or add to the template of information they wish to capture and how things are interrelated.

An add-on tool called SA/Publisher is used to publish websites based on SQL-based queries of the repository using System Architect’s reporting language.