Hilary, I wouldn't get too stressed about instilling bad habits for life. Your sons are still so young. In my book, any tidying up they do at their ages is a plus. Just thank your lucky stars they are doing some tidying and praise them like mad when they do it.
IMO damage limitation is your best bet at the moment. To stop the tide of toys engulfing your sitting room, keep most toys packed away in their bedroom, and rotate their downstairs toys regularly, apart from a few favourites. When your sons make a mess downstairs, at least it will then be a small mess and a lot less daunting for them to clear up.
Also, if they play in their bedroom and you want them to tidy up there, try and make sure you have a definite hidy hole for each toy, or toy group (ie one box for all small cars etc) and your sons know where everything belongs. The more specific you are the better, IME. It's easier to say put all the teddybears in the basket than to say tidy the floor.
As for instilling good and bad habits - well my oldest (7 years) was reallly lazy about tidying away his toys. He still can be, but now he is definitely old enough to be told very firmly to go to it or else.
I have also noticed in him and his friends a sudden new instinct to be helpful around the home. In the last few months he will insist on joining in and helping me polish, hoover and wash up. He actually likes being set chores to do. He pesters me to let him go the our local shop and buy a pint of milk. Amazing! The results aren't always great, but the eagerness is there, so I encourage it all I can.
So just to offer some reassurance for you, IME, an untidy 3 year old doesn't necessarly lead to a chore-avoiding 7 year old.