it is a normal reaction when settling them into your home for them to hide a lot of the time. To help them get around the hutch I provided them with tunnels and hides they could bolt into when they felt the need to and make them feel secure in their environment. After a month I found they grew in confidence and were spending far too much time under the hides so I gradually removed them all - taking one out each week. This was in the top section of their two level hutch and again I put in stools and hides when I moved them inside for the winter as it was a change of environment to them, lots of alien noises and more contact with us on the whole. I do have two stools in the base section of the hutch which I put back after they had got more and more confident, they didnt run and hide underneath them as much, often opting to stand out in the middle where I couldnt miss them and hear their very loud shouts for veg. It takes time and consistency for them to get used to you and your routine, even my very well handled pair of boys took some weeks to get confident with my home and routine, after all the didnt know me from anyone else so I had to gain their trust, I can catch the boys much easier than the herd but they still are silly when trying to stroke them in their pen.
Regarding the food, mine I discovered wouldnt touch pellets, no matter how much I wanted them to have complete dry food I had to resort to muesli which at least meant they were eating something. And now they have also decided they quite like nuggets/pellets as well as their muesli rolleyes. Hay will take up a great percentage of their food, veg at least once daily is important for their vit c intake and then the dry food, which mine have days when they eat the lot, some when they pick at it (although at the moment they are aided by the slugs and snails that keep eating it too).
Handling as often as possible, and try to make it a rewarding experience to them, bribery with their fav veg (you could make this their veg time each day) always goes down well. They will run away when you go to pick them up, I still have the run around with my herd, only the boy is easier to pick up and occasionally one of the girls will get stroppy with me and can be a little difficult but as long as you are able to hold, carry and examine each pig (as in check nails, trim nails, check bums, eyes and ears - I can also check front teeth) then that is all the handling they really need to have.
Dont get upset if they are a little skittish, regular handling will calm them down and only recently I have been able to touch two out of 4 of mine on their noses through the bars, I have had them for over a year - I can hold and examine and have been able to hand feed two out of 4, the other two wont take from my hands but will come near the front now. They will go at their own rate, some take to cuddles much quicker than others, my pair of boys are little monkeys during lap time, my herd rather like being left alone.