Hi there!
I don't know if this response is a bit too late for you to act on, but hopefully it may give you or others some insight.
We're going to Russia the end of April/May and decided to arrange the visas ourselves. We were a little bit worried about registering our visas in places that hadn't issued the invitations which is why we went for the DIY option, (although don't know if that was a valid concern).
Anyway, you only need one invitation from one establishment in order to obtain a visa. In our case we got it from St Petersburg as this is our first entry point into Russia. We're big hostel fans and wouldn't think of staying anywhere else, which wasn't a problem because a number of hostels offered the visa support documents service. For instance, we used Hostel Na Sadovoy who were excellent in providing us with our tourist voucher and authorised accommodation info for around £20. Other St Petersburg hostels that do this are Nord Hostel, St Petersburg International and All Seasons. Godzillas in Moscow also offer a similar service i think.
The whole visa process has been surprisingly easy (we are UK citizens and applied at the Russian embassy in London). I'm sure everyone has different experiences but after sending off our passports, application form, photo, postal order and visa support documents we received our Russian tourist visas back within two weeks. Plus, it has been slightly cheaper than going through an agency, which is a bonus. You hear all sorts of horror stories with visas but i guess sometimes it can go without a hitch! How we get on when we have to register them in Russia is another matter of course!
I hope this has helped someone!