Where new roof shingles meet old, how to fix poor seal

My other answer only answered "what should I put under the shingles". I reread the question and see that @Vebjorn asked how to install shingles. Doing a shed is a good project if you haven't shingled before. Doing a house is harder because of the peaks and valleys.

To shingle your shed, assuming a straight gable roof:

A. Roofing felt.

1. Buy a roll of roofing felt: you can get that at Home Depot or wherever.
2. Starting at the bottom of the roof, staple down a layer of roofing felt. Just roll it out, then use a staple gun to fasten it at the top, bottom and middle about every 2 feet along.
3. After the first layer is put down, add a second layer. Overlap the first layer by about 6 inches.

B. Shingles

1. Start with a layer of upside down shingles, with the tabs cut off. Ask the person at Home Depot for a knife for cutting the shingles - it'll be so dull and gross afterwards you won't want it for anything else. Position the shingles so the overhang the sides and leading edge of the roof by about 1/2". Nail the 1/2 shingles with the strip of tar at the base of the roof, putting nails in the shingle 4 across, top and bottom, i.e. eight nails per shingle.
2. Measure the width of the uncut shingle. Measure that length from bottom of the 1/2 row of shingles on each side of the roof and make a mark. Snap a chalkline between those marks.
3. Do the first "real" course of shingles. Again, overhang by about 1/2". Put 4 nails per shingle, about 1" above the cuts that define the tabs. Put one nail on each side, and one above each tab cut. Use the chalkline to keep them straight.
4. Now the second course. You want each shingle to be offset by 1/2 tab from the shingles below, and up by 1/2 a shingle width. On the sides of the shingle are little cuts: bend the top part and that will give you a reference to "butt" against the lower shingle. That will keep your shingles level. Likewise, there is a cut on the top of the shingle, in the middle of the tab. Bend that up on the first row of shingle (already nailed to the roof). That will give you a place to butt the new shingle side-to-side, to ensure that the new shingle is well placed horizontally. After the first one is placed you can just butt the shingles against each other, so only the tabs on the new shingle are necessary.
5. When you get to the end, cut off the flap as best you can straight with the line you want. Then go back and do the gap at the beginning: you can often use the cutoff from the end you finished to fill in the end you started. (It probably wasn't clear in (4), but I like to start with a full shingle, then come back and fill in the bit at the beginning of the course).
6. Continue until you get to the top. The last shingle should fold over to the other side. Then do the other side.

C. The peak

1. Now you have two sides of shingles folded over. You need to finish the peak.
2. Cut a shingle into three tabs, cutting up-and-down at the tab slot.
3. Turn a tab sideways, and fold it over the peak at one edge of the building. Choose the edge away from the prevailing wind. It should be half-and-half on each side.
4. Measure how far down the peak it goes, the mark the same distance from the peak on the other side. Snap a chalk line.
5. Continue to nail tabs (1/3 shingles) along the peak, two nails per tab, using the chalkline to line them up. You won't have the tabs to help you with the offset now, but by now your eye will be pretty good. :)
6. Finish up with a 1/2 tab. Tar the exposed nails.

Bubbles in a roof like this are NOT normal. They indicate a problem underneath. Is it serious? Possibly. It will probably decrease the life of the roof.

The shingles will have been nailed down, so this is not a case of the shingles simply pulling loose. Especially if the roof is soft there, it seems this must be a case of the plywood underneath having gotten wet and as it dried out, then warping and bubbling up underneath. The plywood should have been replaced where there were problems.

Edit: After seeing the interior picture, it looks like there was some water contact there at some time. Is it still happening, or is this old, perhaps when you had the hail damage? I find it useful to use a moisture detector - Wagner Moisture meters. It is something I have for woodturning purposes, but it is useful to resolve problems like this. You may be able to rent one, since it hardly seems worth buying one for one use though.

If there is still moisture there, it is possible that water is still getting in, that the roofer made a mistake somewhere. Water can be insidious that way, getting in the tiniest of cracks.