Add more usage documentation (#1)

Author: sirno

README.md

@@ -43,8 +43,15 @@ virolution = "0.5"
 
 ### Basic Usage as a Binary
 
-After installation, you can run the binary with a sequence file and a configuration file. A
-configuration file may look like this:
+To find all available options and their default values, you can run:
+
+```shell
+virolution --help
+```
+
+The simulation can be run with a sequence file and a configuration file. A configuration file
+provides the parameters for the simulation environment and the schedule for any events during
+the simulation. It may look like this:
 
 ```yaml
 parameters:
@@ -94,7 +101,12 @@ between two compartments. The sample event will occur every 200 generations and
 the current generation number and an event will be executed whenever the expression evaluates
 to 0.
 
-There are more events that can be configured in the schedule.
+There are more parameters and events that can be configured in the schedule. For more information
+on the configuration, see the [documentation](https://docs.rs/virolution/latest/virolution/config/index.html).
+
+When the simulation is complete (reached its maximum generation), the final population will be
+stored in a file called `final.<i>.csv`, where `<i>` is the compartment number. The file will
+contain all haplotypes and their respective counts.
 
 ### Basic Usage as a Library