Those numbers are your overall modifier for that skill or saving throw. They include your proficiency bonus if you are proficient in them, otherwise they are just your ability modifier for that skill or saving throw. They're pre-calculated and listed on the sheet for convenience during the game so that you don't have to add up all your modifiers and Proficiency bonus every time that roll is made.
So if your example Cleric is proficient in Wisdom saving throws and has a Wisdom score of 15, their Wisdom saving throw modifier = proficiency bonus (+2) + Wisdom modifier (+2) = +4, which is the number that will be listed under Wisdom saving throws.
On the other hand, your Cleric probably doesn't have proficiency with Dexterity saving throws, and let's say their Dexterity score is 8. Their Dexterity saving throw modifier = no proficiency bonus (+0) + Dexterity modifier (-1) = -1.
There are other factors that can affect this calculation, such as the Rogue's Expertise feature, but this is the basic calculation that will be used in the vast majority of cases.
Not without larger changes.
A RAW interpretation of the UA Beast Ranger says no, there are no flying animals in the list of creatures, so adding a fly speed would not fit the pattern.
However, for the purpose of trying to say yes to player requests for options (AKA, with DM approval), here is my analysis of the Owl/Giant Owl stat blocks as ranger companions.
The Flyby ability of the Owl and Giant Owl are significantly more powerful for a combat proficient creature than anything else available for UA animal companions. Combining this with a flyspeed of 60ft, and they could fly in, attack, and fly out without taking an attack. This effectively makes them untouchable by melee combatants.
This feature is also not comparable to the abilities of other animal companions such as: Keen Smell, Charge, Relentless, Sure-footed, and Pack Tactics.
Also, the other animal companions have a 40ft walking speed, and do not have darkvision.
All in all, this companion is objectively better than the other UA companion options. 120ft darkvision, 60ft fly speed, and the flyby ability are all individually more powerful than the standard companion.
I would start by removing/reducing all of these features. Limit the darkvision to 60ft, reduce the flyspeed to 40ft, and eliminate the flyby ability. Then reduce it to fit the UA rules on companions. Do not replace flyby with a new ability, since you still have some darkvision and a fly speed.
Remember, the UA Beast Ranger is a bit OP compared to the other ranger archetypes, with an effective multi-attack at level 3, plus a pseudo-multiattack on top of this at level 5, so you should err on the side of underpowered when creating a new ranger companion option.
Best Answer
Let's look at your wolf first. A base wolf has AC 13, 11 hp, proficiency in Perception and Stealth, and not much more to help in its survival. UA Ranger's Companion's Bond gives it some considerable benefits at level 3, first of them being the ability to add your proficiency bonus to its AC and damage rolls, in addition to its skills, saving throws, and attacks it has proficiency with. Next, it gains two skill proficiencies and becomes proficient in all saving throws. Oh, plus all benefits of your Favored enemy.
What all of this means is that your wolf has AC 15, still 11 hp, but is proficient in all saving throws and has some skills that may help it further. As you gain levels, your beast will increase its maximum hp and proficiency bonus (applied to its AC, saves, skills, attack and damage rolls) at a rate similar to yours, and with a d8 Hit Die, it will not fall far behind. Sure, now it might have less than half your maximum hp, but at later levels it might have more than your party's Wizard or Bard. And even if it dies, you can call it back using 8 hours (can be done during other PC's long rest) and 25gp - to compare, a Potion of Healing (2d4+2) would cost at least twice that.
Now, how to keep it alive. You might have to employ some clever tactical thinking here, but even at 3rd level it should survive one or two blows from the enemy brutes, maybe even a spell. And if it gets hurt, you can just tell it to Disengage and retreat, and take a rest or heal it directly afterwards. As for tactics, a few come to mind:
1) Hit and Run/Assassinate. This utilizes the wolf's Stealth proficiency and comes down to it striking from the enemy's blind spot, Biting to knock the target prone and running away if it finds the situation too dangerous for its liking.
2) Keep it close. If you fight as a duo, you never have to worry about your companion being too far away to be healed, or getting surrounded without anybody to provide help. If you're a Halfling or a Gnome, you might even want to consider riding it into battle!
There are also some other points that may help. First, wolf's Bite can knock its target prone. This gives the wolf, you, and any other ally attacking this target advantage on attacks against it (while within 5', otherwise disadvantage), while having the prone target attack at disadvantage. This heavily shifts the balance in favor of the wolf, even when fighting 1v1. Second, Keen Hearing and Smell paired with proficiency in Perception means that the wolf can notice danger much faster than others, and will rarely be surprised. Third, Pack Tactics, which can help you quickly dispatch a powerful opponent together or curb the numbers of an uneven fight to better match your preferences, especially when paired with a successful knockdown on Bite.
To summarize, your best bet seems to either utilize the wolf's heightened awareness and Stealth to keep it out of harm's way, or heeding the saying "the best defense is a good offence", neutralizing your foes before they have a chance to do any serious damage.