You haven't specified if you have Russian visa too or country of your citizenship - formally, you have to obtain separate visas in both countries.
But there is no passport control on the border between Belarus and Russia (only random checks), so I think on departure from Russia only first entry stamp date (the date you've entered Belarus) will be taken into account.
Answer from US Embassy on similar question on stackexchange - Do I need a visa to visit Belarus if I have a Russian visa?
For boarding the train or plane you have to show passport with valid visas. There is no passport check inside the train when it passes Belarus/Russia border. Flights between Belarus and Russia are considered domestic.
UPD2: There is a bunch of different rules for different countries even from CIS bloc and I cannot find any clear information about such case neither on Belarus foreign affairs ministry site, nor on the Russian one. But I suggest a solution: you may register as soon as your arrive to Russia - it's not obligatory for citizens of some countries, and for others your hotel or host have to do it for you. Ask to get the paper with this registration date and you could show it on exit border as a proof that you stay in Russia from this date and had a right to stay for number of days. According to this you even have to keep this paper with you until you leave the country.