Well, assuming you know how to install tomatocart it should be very simple. You have web site for example
example.com you have installation files for tomatocart, you will go to ftp of your site you create there folders let say test1 and test2 then you copy full installation to test1 folder and then copy it again to test2 folder. Now you are almost ready, you open explorer you go to url address
example.com/test1/ this will start installation of tomato cart to folder test1 you will install it you will set database and installation wizard will ask you for Database Table Prefix The prefix to use for the database tables. For example you will set this to tomato1_ and continue to end of installation. Now you have store in
example.com/test1/ and administration in
example.com/test1/admin/ in database you will have store tables which will all start with prefix tomato1_
Now to set store 2 you wil go to url
example.com/test2/ start installation and do all same like before for store 1 except when you will be asked for table prefix you must set something different for example tomato2_ when you will finish installation you will have 2 different stores each with own administration one will be at
example.com/test1 and other store will be at
example.com/test2
You can of course make folders with any name, not just test1 or test2

what prefix in database you will set doesn't matter as long as there will be no spaces or some special characters just stay with A-Z 0-9 and under score _ To make sure I am correct I just done it all now so I could easly describe how to make it.
Btw right now in last version when you navigate in store there are links on top of screen Top » Online Shop
second link will take you to directory of your actual store so if you will be in test2 second link Online Shop will be like
example.com/test2/index.php that's ok but first link in navigation Top will take you to root of website it mean to
example.com/ and because you have in this root only folder test1 and folder test2 this can lead to something bad. You can always put into root of web some index.php or index.html with links to store 1 and store 2.
I seen in code repository this first link 'Top' leading to root of website will be removed.