Hakone to Agematsu

we will be travelling from Hokone to the Kiso valley for one night only, staying in Agematsu hoping to walk from Magome to Tsumago on to our hotel , the next day travel on to Kyoto.
what is the best and cheapest way to do this please

Best and cheapest are not often the same. From Hakone to Agematsu is not a simple straight line as both have access issues, so you might chose a bus or train (or combination), but it is going to take a while.
My quick search for buses versus trains suggested some pretty horrible routes including a 5 1/2 hour over-night bus (because of the time of day here in Tokyo), or a fairly long train ride (but cheaper than the bus).

What I would normally recommend is rearrange your travel so that you departure/destination for both Hakone and Agematsu are easier to get to. Hakone is accessible from Tokyo, Agematsu is accessible from Kyoto/Nagoya (well, slightly more accessible). Heading to those obscure places in the alps simply takes time.

Thank you for your email, i had thought about going from Odawara to Nagoya Station then the ltd express train to Nakatsugawa station, a bus to Magome walk the trail to Tsumago station train or bus to Nagiso , then on to Agematsu.
Is this possible to do in one day as i havn't looked at the times for travel
Thanking you in advance