Great question!
I'm not sure about a standard way, or even a way that might be considered best practice yet. But I use all of the tools you mention to perform very similar tasks.
To try and answer your question: What I do is create the U-SQL scripts as stored procedures within the logical ADLA database. In the VS USQL project I have 1 script per stored proc. The ADF activities then call the proc name. This gives you the right level of disconnection between services and also means you don't need additional blob storage for USQL files.
In my VS solution I often also have a PowerShell project to help manage things. Specifically one what takes all my 'usp_' U-SQL scripts to create one big DDL style thing that can be deployed to the logical ADLA database.
The PowerShell then does the deployment for me using the submit job cmdlet. Example below.
Submit-AzureRmDataLakeAnalyticsJob `
-Name $JobName `
-AccountName $DLAnalytics `
–Script $USQLProcDeployAll `
-DegreeOfParallelism $DLAnalyticsDoP
Hope this gives you a steer. I also accept that these tools are still fairly new. So open to other suggestions.
Cheers