present or past perfect? or past simple or present continuous?

i hate tenses. to my core.

czech (though not an easy language) has three tenses. they're called past, present, and future.

so it's hard for them to differentiate between our different tenses - or to figure out when each tense is correct to use.

for example:

present simple: i run
present continuous: i am running
present perfect: i have run

(note how present perfect uses present tense "have," but past tense "run")

so, how do you tell people who are learning english when to use each of these? thankfully someone else came up with the rules. i have them copied down somewhere in case someone asks me.

last week i taught a lesson (singular lesson; i refuse to teach more on this terrible topic) about tenses, and we had an argument in class about several things, namely the following:

a) What were you talking about when I (come)____ in? Of course the correct form is came, but the argument was about why it couldn't be "was coming"

b) How long have you lived on your own
   1. in this flat?
   2. before you met Lisa?
well?

c) (fill in with correct past or present perfect form of have)
Carla says she ____ sent the email, but I'm sure she _____ because I've checked three times and it's not there.
my certain tough student argued that it should be past tense "had" because of the verb "checked"

uff. i can answer these questions (and will, if you so desire). but come on...how annoying are tenses?