Yes, just apply for it with a few days buffer either side. I've done this twice. The first time I entered as expected as it was very much a holiday. The second time I was travelling up Finland to the arctic circle, and then crossing there. The buses from Rovaniemi were not every day, so I ended up bussing to Ivalo, and then to Murmansk, getting there a couple of days later than planned.
The only confusion at the border was that I was a Kiwi arriving on a Russian bus company from somewhere in Finland. And on a Russian business visa. But once the border guy was over that, there were no problems. Point is, I arrived a couple of days into the period my visa was valid for. And there is no problem with that - it's just a maximum period of validity, not a fixed arrival/exit date.
All websites will tell you - DO NOT book flights before applying for the visa, in case you don't get it. However if you want to in order to save money, you might still consider doing it - I certainly did the first time. It's a calculated risk, if you're going as a tourist, have no criminal issues or problems that may give them problems with giving you a visa, have an invite and have travel insurance, there's very little theoretical chance of them denying you. However, stranger things have happened.
Personally I never book accommodation more than a few days in advance - which has caused me some grief (I got the very last bed at the hostel I'm staying at in Seattle this weekend), but one thing to be aware of with Russia is that they often ask where you're staying. Last time I wasn't sure, and just put the 5 biggest cities I was likely going through. That worked fine, and the cities aren't listed on your actual visa.
If you're worried and are happy with hostels, you can always just book one with Hostelbookers and if you don't get your visa, email them and cancel your booking. You only lose your 10% deposit.