Hi vinagi, and welcome to MySwissAlps!
>> Can you advice which direction is better - Biel, Interlaken or other?
That depends on what you mean by better ;-)
The fastest way, which the timetable will suggest by default, takes around 2.75 hours, and goes via Biel/Bienne, Olten or Bern. If your connection involves a change of trains at Biel/Bienne or at Bern, changing trains just means walking to the other side of the same platform. If you need to change trains at Olten, you need to walk from Platform 12 to Platform 8 - two platforms over. This route is pleasant, with flatish or undulating countryside, and not especially scenic.
A route with mountain, lake and traditional village scenery - which would take 5.5 to 6 hours - would be to go via part of the Golden Pass route: Basel > Spiez > Zweisimmen > Montreux > Genève
If you had all day, you could incorporate the full Golden Pass route, which would take 8 to 8.25 hours: Basel > Luzern > Interlaken Ost > Zweisimmen > Montreux > Genève
All these routes are free with the Swiss Travel Pass.
>> On all the itineraries I see dotted line, which means I have to pay extra. When and where I do that?
I think what you are probably looking at are dashed lines, depicting tunnels. These trains are free with the Swiss Travel Pass.
You can plan this trip and check your options using the Swiss Timetable. To travel by a scenic route, you will need to put the stations I noted above into the "via" fields of the timetable.