>> I wanted to ask experts here if hiring apartments little away from the main town will be difficult to commute?
When considering which accommodation to choose, look up the address in Google Maps, then zoom in to find nearby railway stations and bus stops. If you hover the mouse over the bus stop or railway station logo (or tap it on a hand-held device), it will give you details about the official name of the stop, and for buses, the number/s of the bus routes that stop there. You can then use that information in the official Swiss Timetable to find out how frequent the service is, and at what time the first and last connections for the day run. As Chantal has already mentioned, make sure the transport options for evenings and weekends in particular will suit you.
>> As suggested in some forums if we book either in Lauterbrunnen or Grindelwald instead of Interlaken wont it be difficult to connect?
It will be very easy as long as you are close to transport that meets your needs.
Lauterbrunnen has a railway station and a regular bus service (#141) that runs along the valley from Lauterbrunnen railway station to Stechelberg. The bus service operates from early until late at half-hourly intervals (hourly after 19:35).
Grindelwald is hilly and very spread out, and the town bus service only runs until early evening, so you might prefer to find somewhere within a comfortable walk from Grindelwald railway station.
>> We also found some nice stay options near Thun. Can we stay there & make it a base instead of staying in Interlaken.
Likewise, find out where your accommodation is in relation to Thun railway station, or to any bus services. If you would be relying on a bus, find out what time the first and last services of the day run, how frequent the service is, and whether weekend and evening services would meet your needs.
Something to be aware of with addresses is that Bern and Luzern (for example) are the names of cantons as well as cities, so when you see "Luzern" in an address, particularly if it is not a hotel, it might not actually be in the city of Luzern, but could in fact be in a more remote part of canton Luzern: so finding the address on a map is a good way to ensure you know exactly where it is, and what transport is nearby, before you book.