First you need to setup a Linqer Connection.
Linqer Connection Pool screen pops up, when you run program first time.
Click Add button to create a new Linqer Connection.
Specify a Connection Name (for example Northwind).
Specify a Connection String to connect to a SQL Server database.
If you already have a Visual Studio project with LINQ to SQL classes you can specify paths for *.dml and *.designer.cs files. You can also generate these files using SqlMetal tool by clicking Generate LINQ to SQL Files button.
Specify a Data Context Variable, which can be used in the produced LINQ statements.
As soon as you setup a Linqer Connection you can convert SQL to LINQ.
You can have more than one Linqer Connection and pick the active one from the Connection list on the main toolbar.
You can type, paste, or load SQL statement from file into the SQL window.
Click F5 or use convert button 
to produce LINQ statement.
Click F7 or use Run button 
to compile and execute LINQ statement.
The query result appears on the bottom section of the screen.
You can compare the output SQL, which has been produced by the .NET with the original SQL statement.
Code for DataContext variable declaration can be obtained at the Data Context section.
Click F6 to or use compile button 
, in case you don't want to run LINQ statement, but just want to make sure it is valid.
Use copy to clipboard button 
to move generated LINQ expression into your Visual Studio project.
Use generated classes, which turn your query result into the convenient list.
Use 
button to replace class names. Copy to clipboard button helps you to move generated classes into your Visual Studio project.