I would like to sell some euros in an online exchange and buy rubles. My question is, once I buy rubles how do I withdraw them in my Russian account? Also, how to deposit euros? I know about some services that use agencies, but I doubt it's practical to go around with millions of rubles.
There are two components to this - the currency conversion and the transfer between your two accounts. If you just do the transfer, the banks will do the currency conversion for you, though not without fees and not necessarily at as good a rate as you could get elsewhere.
If you use another service to do the currency conversion, you will need to transfer your euros to your account with them from your euro-demominated account, then transfer your resulting rubles to your ruble-denominated account. Normally there's some paperwork involved in getting the destination account set up with the exchange, due to money laundering regulations.
As you'll have noticed, you're now doing two transfers, both of which will have fees, so you'll need to be certain you're making enough on the better exchange rate to cover that.