I did Moscow to St Petersburg last January on one of the day Sapsan services.
Although I speak no Russian, I managed to navigate the Russian Railways website at
http://rzd.ru/ with the aid of Google Translate.
The fares were lower (unsurprisingly) than using an agent, and eTickets were issued. The whole process was quite a lot of fun and had something of a sense of achievement beyond the usual!
I would also recommend
Real Russia for visa applications, and you could, of course, use their rail booking engine to research what you're looking for, and then go to Russian Railways to complete the booking.