Here is a part from the playertech.entity file

NonCombat
  blockCount 3
  block
   area [ 50 , 93 , 690 , 192 ]
   backdrop "ResearchScreenBlockBackdropNonCombat0Tech"
   tierIndicatorBackdrop "ResearchScreenBlockTierIndicatorNonCombat0Tech"
   title "IDSResearchScreenBlockTitleNonCombat0Tech"
   picture "ResearchScreenBlockPictureNonCombat0Tech"
  block
   area [ 50 , 295 , 690 , 192 ]
   backdrop "ResearchScreenBlockBackdropNonCombat1Tech"
   tierIndicatorBackdrop "ResearchScreenBlockTierIndicatorNonCombat1Tech"
   title "IDSResearchScreenBlockTitleNonCombat1Tech"
   picture "ResearchScreenBlockPictureNonCombat1Tech"
  

I will rewrite the definitions of the numbers which are:   
 [ (Left Position) , (Top Position) , (Right Position) , (Size of Block) ]

In order to determine the nessary top position that the second block needs so it does not intersect the first block, add the 2nd number along with the 4th number and an additional 10 for spacing between blocks.  So, 93+192+10=295

If you need more explanation than this please let me know

Unfortunatly the number of blocks in a research tree are hardcoded as far as I am aware.  I have tried to put in an additional block in the defense tree since the start of the entrenchment beta, as well as looked for a way to add blocks to the fleet tree within my mod, but no matter what I try or how I try to rig it, I am still unsucessful

Yeah, I will, but cannot think straight at the moment.  Spent the last few hours working on my mod and right now I am in serious need of sleep.  Will get those to you tomorrow evening when I jump on after work.