I've done SQL Server heavily at work but at home I keep 20 personal databases, so daily I've seen both worlds. I've modified a single practice, and it's the workhorse I use constantly in Access:
After initial setup of whatever quickies I can do in Design View, I copy to Notepad and refine the query from there.
In fact I version-control records in a table called "QueryArchive," where I plop a starting copy of any query I'm about to modify. I designed the table so the records are timedatestamped, have a comment (what i worked on, what I need to write later, etc.) and have a yes/no box to indicate if a version went to "prod" (that is, if I actually copy that code version to its named Access query where I execute it).
In short, I use Design View for quick config tweaks, but Notepad for the heavy development--Notepad and my table QueryArchive KEEP the formatting.
In spite of my best coding efforts, there will be that most-complicated project where Design View craps the bed--it's one reason I keep this practice : I can unendingly pull the fresh copy of my initial code in its unaltered format.
The other reason ? This practice is dead-simple: No code mod !