Question 1: diffence of meaning (of up)
Answer: 'up' as an adverb used following a verb means
(a) to a disired or better situation,
(b) to an end.
tidy up/wrap up/phone up
line up/set up
In sense (b), verbs collocate with different adverbs: up/out/off, sometimes two of them are interchangeable.
When you use 'up', relative to not using it, you put a slight emphasis onto your meanig.
Question 2: when to and when not to use 'up'?
For a certain sense of some verbs , the 'up' is optional. There seems to be no obvious regularity which verbs can(not) be used with 'up' , or rather if you want to give a stress, you add 'up' to them.
On the contrary, for some other verbs, the verb alone and the struction of ' verb + up' may be different words, with the latter called a 'phrasal verb', for example, set vs set up.