Is your score positive? You win! (Some players win more than others.)
A woman needs a man like a fish needs a saxophone.
does it means there's 2 seperate ER, each time the nation can build new trading post and buy new ship?
does it also means there'll be 2 rounds of merchant payments before we have another round of MR?
Yes. Note that in the first ER, none of the countries have ships, so there won't be any merchant payments. (You'll still collect for your P0-P5 cards twice, unless you use them.)
and does the phase 1,2, 3 which impacts the number of hex for the discovery ship has anything to do with MR1, MR2 etc?
No. Merchant rounds are completely unrelated to game phases 1-4. Phase changes are triggered as soon as the appropriate ship is bought (or scrapped at the end of MR 2 and up).
this rule book is one of the worse i have ever read. very bad from zman games. not typical of it at all.
I found it to be reasonably clear myself. Some of the concepts are a bit obtuse if you're unfamiliar with 18xx games (as I was). It's a pain in the neck but reading through everyone else's rules questions actually gave me a better feel for how the game goes.
Then again, I also didn't have any problem with the legendarily bad Phoenicia rulebook.