Can someone help me figure out the holy sonnet 1 on this website. I have been trying for the past couple hours and only have half of it done. I do know all the lines are iambic pentameter, but I am struggling with the stress check and feet check. http://prosody.lib.virginia.edu/prosody_poem/holy-sonnet-1/

First off, I can say that from the perspective of a university-level poetry professor, your frustration with understanding meter is totally common; my students frequently struggle to understand how to scan poems! You are certainly not alone! In order to successfully identify poems you need two things:
1) First, you stated that you know that this sonnet is written in iambic pentameter, but it is critical to understand what iambic pentameter means. Let us look at the first part of this phrase: "iambic."
An "iamb" is a type of "foot" in poetry, and a foot is merely a pairing of two syllables. An iamb is a foot in which the first syllable is unstressed and the second syllable is stressed. As a result, in the first "foot" or "iamb" of the poem ("Thou hast"), we can deduce that the first syllable is unstressed ("Thou") and the second syllable is stressed ("hast"). Since this whole sonnet is iambic, we can say that this pattern is true for ALL of the syllable pairings here. 
We can deduce what "pentameter" means from the prefix of the word itself. "Penta-" means "five." Thus, we know that the meter of this poem involves five iambs per line.
2) Another thing that helps my students is reading the poem out loud to listen to what syllables are stressed and unstressed. Try doing so while placing your hand over your heart. Iambic pentameter sounds a lot like our heartbeat: lub-DUB, lub-DUB, unstressed, STRESSED, unstressed, STRESSED.  
With these tidbits in mind, let us now look at the scansion of the poem. I have broken it down below as follows:
unstressed syllables are italicized

stressed syllables are CAPITALIZED
iambs are separated by a single bold line ( | )
Thou HAST  |  made ME, |  and SHALL  |  Thy WORK  |  deCAY ?RePAIR  |  me NOW,  |  for NOW  |  mine END  |  doth HASTE;I RUN  |  to DEATH,  |  and DEATH  |  meets ME  |  as FAST,And ALL  |  my PLEA-  |  sures ARE  |  like YES-  |  terDAY.I DARE  |  not MOVE  |  my DIM  |  eyes AN-  |  y WAY;DesPAIR  |  beHIND,  |  and DEATH  |  beFORE  |  doth CASTSuch TER-  |  ror, AND  |  my FEE-  |  ble FLESH  |  doth WASTEBy SIN | in IT, | which IT | towards HELL | doth WEIGH.OnLY | Thou ART | aBOVE | and WHEN | towards THEEBy THY  |  leave I  |  can LOOK,  |  I RISE  |  aGAIN ;But OUR  |  old SUB-  |  tle FOE  |  so TEMP-  |  teth ME,That NOT  |  one HOUR  |  mySELF  |  I CAN  |  susTAIN.Thy GRACE  |  may WING  |  me TO  |  preVENT  |  his ARTAnd THOU  |  like AD-  |  aMANT  |  draw MINE  |  iron HEART.