Hi Parvathi.. Depends on your budget.. You can take a connecting flights to Kullu which is about 40km from Manali. Or you can go by train but its would take nearly 2 days I suppose. So it would be better to split up and go via flight to Delhi and from there its an overnight bus travel to Manali. However, in case you have motion sickness, I would suggest take a train from Delhi to Kalka and from there you can jump on to a toy train to Shimla and experience the scenic beauty along the trail. A lot of options depending on your budget and preferences :)
With respect to accommodation, there are many 3 star hotels in both Manali and Shimla and you can easily book them from goibibo or booking.com. Would suggest to book something close to the market so that you can easily get Transport to go from one place to the other. In case you are traveling with friends, you can also opt for Hostel stay like Zostel. Hope this helps!
There are two routes one directly from Delhi an one from chandigarh..I would suggest you go from chandigarh and from there reach manali it's a 6 hour drive then you can explore manali for a day or two then go to manikarn, and you can enjoy rafting there you can also visit mandi, kullu with this then reach shimla...there are lots of places to explore there