No problem with doing this and no need to mention on entry into Malawi.
We flew back several times (for between 2 and 6 weeks at a time) over a year and left the car each time. As long as your carnet is valid the car /bike can be in country. Don't say anything on entering the country, it may cause confusion.
As to where to leave it I'd suggest asking somewhere you stay. There are a few lakeside places that would probably oblige. It's less likely in Lilongwe where parking is at more of a premium, though you could try Mabuya (lodge/backpackers).
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