Welcome to bulbs. Does it matter which side goes up? Most definitely. In general the pointed end goes up. Most bulbs will have some roots even if tiny on the bottom and a point on top. The bottom is usually wider. Tulips, Daffodil, lily, others all have a narrower or pointed top. But don't have a fit if you make a mistake with a few. The bulb will grow anyway even if you get a few upside down, though it will take those a bit longer to sprout. Things like Irises which have rhyzomes need to be planted only half covered. Otherwise pointed or narrow end up.
Depth? example...The info on tulips states a required 6" depth. If you get some at 5" or 7" or 4" they will grow. You won't kill them by being off a little. But try to stay at the desired depth. Its given for a reason. A few bulbs can be way off and do very well. Example Lilium....Lilies will pull themselves down to the desired depth even if planted half out of the ground. I don't know any others that do this. Do not plant any bulbs too deep. Its better too shallow than deep if you must make and error. Remember to figure on the thickness of the mulch if you plan to use one. (the settled thickness) Mulch will keep weeds down to almost none. Contrary to popular thought, winter hardy bulbs (tulips, daff, lily, crocus, etc) are NOT planted deep to protect them from the cold. The depth is to protect then from the summer heat. Don't water them when you plant. There should be enough autuum rain. Overwatering can rot them. Your planting idea is the way I started my bulb garden tho I can't do it now with everything there. You can remove the top 5" of soil, set in the bulbs, then put in your compost. WARNING....you will need to place a few handfuls of soil around each bulb or they will flop over on their sides when you toss the compost in. I would mix the original soil with the compost and use that. My own mixture is sand, peat, compost and a bit if top soil. Heavy on the peat. Works good for me.
Next spring? Leave the bulbs right where they grow. After the foliage turns brown you can cut that off and plant whatever you like. Don't cut off the foliage before it dies or you most likely will not see those again. The leaves need to stay growing to store enough food in the bulb for next year. The roots of the second group won't bother the bulbs. You don't need to pull them to plant your annuals. Why do all that work just to put them back in the fall? You are in zone 5. I assume you did your homework and know wheather what you have can stand the frozen winter ground? Do you have Dahlias? They need to be stored warm over winter. If you add perrenials later that are NOT bulbs you can leave the roots of those in the ground also. If what you but can stand the cold you should leave it in. Unless you can afford to trash them each year.Hope this helps.

Some bulb species start growing their roots long before you see anything above ground. Narcissus/daffodil for one. If you live in an area where the end of summer is dry and the ground starts to cool down quickly then you actually might need to water your bulbs to get them growing underground. (I think this can be the case in Minnesota.)

If you want to take out some of the bulbs next growing season put down a layer of coloured sand (natural) and place the bulbs onto that. That makes a marker for when you're digging latter (oops! yellow sand! I'm on the bulb layer - go carefully.)

As you're planting you might want to do it in 'islands', leaving ribbons of unplanted soil between. You see, some bulbs, such as Narcissus Earlicheer, have leaves around 18" high and they can take a long time after flowering to finish their growth cycle. Meantime, the leaves are starting to flop and smother the ground around them - including anything you've planted as a filler. You can prop them up with carnation rings or similar provided you've allowed for that in your planting progression. They're too lush and dense to be disguised with annuals of any but the most exuberant growth.

Block planting of tulips can look very formally effective - and they all finish 'together'. A patch of green slowly turning yellow. It helps to have either a perennial such as a Geranium or an annual such as Myosotis to mask the ending phase of the tulips. If you match your annuals planting plan with your bulb layout you should be able to do this reasonably easily.

If you can count on a good snow layer to act as a protective mulch over the winter you might not need to be concerned about frozen bulbs. If you get wind scour in your yard - adding a layer of mulch that won't fly in the wind could prevent bulb loss.

As you plant your bulbs - draw a plan of what you've put where. Two reasons - you'll know what to expect; and when you come to overplant or interplant, you'll know where to go carefully. A plus is being able to give names to what do well in your garden for future reference.

In addition to lilies, tulips can also dig themselves down to a decent depth as can some of the Narcissus species. As they put down their roots they form 'droppers' which develop a bulb structure over the growing season. When the leaves die down, there's the new bulb - a lot deeper than you planted it.

If you water your annuals regularly over the summer, also take note of which bulbs actually prefer a fairly dry spell of dormancy over the summer - and plant your annuals to suit this need.