I've recently decided to play each Zelda's Game in its official timeline order. Right now I'm doing the alternative timeline which OoT's Link dies, I've just finished aLttP, and now I'm going to play the Oracle Series. So here goes my question.

    Are both games occuring parallel to each other? According to Hyrule Historia, Oracle of Seasons is the first then comes Oracle of Ages. But as I was browsing through some additional info I found out you can direct-link both games to unlock a linear history, should I play the linear history or each game separetely? Thanks in advance!

no. firstly play each game seperatly (the order is not important) you can play seasons or ages.
then in each games end you'll get a code (labrynna secret and Holodrum secret) then start a new game. if you got from ooa the labrynna secret,use it on oos and vice versa. but you probably know this,don't you? you'll get other secrets like the ghost in the Graveyard in Labrynna. he'll tell you to give the secret you got from him to a person in Holodrum. if you're done you'll get a precious Item. If you want that item you got in holodrum to Labrynna, you must go to labrynna and give the code to Farore. she will give you the same item from Hoodrum.
ATTENTION PLEASE
If you got all heartcontainers in a game,skip one secret that includes a heartcontainer as a reward. i did it before and thought i would have 21 heartcontainers but instead if getting a heartcontainer i lost one then i had only 19 left. yeah... so be careful.

Thanks for replying, I found the codes by browsing zeldapedia. If I start playing with those codes instead of starting from the begginning will my final experience be affected?

LucasMull : strange i've heard of the alternate timeline where he dies.....

noahd101 : Here it is, the Nintendo's Official Time line: http://goo.gl/jII5Ep
       After OoT events there were created two timelines, that's because Adult Link was sent to relive his lost childhood after he defeated Ganon in the future. So he basically changes the whole history by warning Child Zelda about Ganondorf intention after his return. AND to complicate everything there is a third time line, which may or may not occur, it's proceeds in a reality in which OoT Adult Link dies by Ganondorf.