In the beginning I would not use a very tuned piece square table but use a more simple one. That should give all your pawns and pieces a general direction and a frame where they belong. The different values on the squares compared to a tuned PST should step by step be explained and achieved by additional positional terms of other evaluation features. All values should always be just big enough and you should take into account the already existing terms. Do not use a high value near a full 100cp value just to forbid your engine to do a stupid move. This would backfire in other positions. As soon as the positional values sum up to a value bigger than a pawn (100cp) the engine may lose that pawn. Make sure it is worth it.
Instead try to see the bigger picture and find a more general evaluation feature. You could start with some simple and easy to write features from different perspectives.
A mobility term where you count every possible move of your pawns and pieces. Every move could be counted as 1cp or you use a different weight depending on the piece, the centralisation or rank of to-squares (this is already a hint of the possibility and probability of the piece's future on a square with a better PST value) or if that square is free, occupied by your opponent (possible attacks) or by own pieces (possible defends) or if the to square is attacked or defended. Give a bonus for attacking weak pawns (see below). That will take some time and should start simple. It can be improved later.
A king safety term that just counts the pawns (and if there are not enough some own minor pieces) around the king (up to 8 squares around it) and pawns on the three squares in front of this area. The king should stay in a corner behind its pawn shield in the middlegame. but that is already achieved by the PST. Instead the pawns are hold back to the fixed king with the king safety evaluation. In a more advanced evaluation you also count the piece attacks and hidden attacks to your king and its pawn shield by enemy pawns and pieces. But that is not so easy to implement for distant sliders. Beware of rooks on (half) open files to or next to your king. Give yourself a penalty or your opponent a bonus for that.
If you have more than one penalty for the king safety give an extra penalty increasing with the number of these penalties.
Passed pawns are very dangerous and should get a high value. But not too high and too optimistic. Rather add some extra centipawns if the passers are defended or are aligned by another own pawn. Check if the square in front of it is free and not attacked. If you have two passers that are many files apart that is also dangerous and should be awarded some points. Give a rook behind your passer a few points
Give some extra points to a player with both bishops.
Take some penalty points for doubled pawns. Increase this if in the center or in your king shield.
Take some penalty points for isolated pawns. Increase this if in the center or in your king shield.
Give some extra points for rooks on (half) open files.
Give some extra points for rooks on the 7th rank especially if there are enemy pawns on that rank and if the enemy king is still on its first two ranks.
Give a bonus for your knights depending on the distance to the enemy king.
Give a bonus for queens and bishops for being on a file or diagonal that leads to the enemy king. You can use precalculated tables for this or calculate real attack rays which is far more complicated.
Give a bonus for minor outposts (unattacked knight or bishop on ranks 4 to 7) especially on the opponent king side and if defended.
Have a look at your pawn structure.
Give penalties for weak pawns (google this specific pattern).
Give a bonus for pawns defending pawns and aligned pawns.
Give a bonus for advanced pawns near the opponent king but don't ruin your king's pawn shield (pawn storm).
Count the blocked pawns (rams) in the center and on both sides. These numbers (closed or open position) may have influence on the weight of other features. (
http://www.fraserheightschess.com/Docum ... _Types.pdf)
Try to detect pins to the king or queen and give that a bonus.
Try to detect x-ray attacks on pieses through pawns or pieces and give that a bonus.
In the opening give a penalty for undeveloped pieces (knights and bishops) on the first rank.
Give a penalty for these pieces in front of pawns on d2, e2.
Do not give a bonus for losing the castle possibilities (that is taken care of in king safety).
Do not give a bonus for keeping the castle possibilities (the engine would avoid castling).
In the endgame (when most pieces are gone) implement the rule of the square (king and enemy passers) with a high penalty.
If the opponent has one bishop only your king should avoid the corner that can be reached by this bishop.
Give a bonus if a piece or the king defends an own passer and the square in front of it.
Give a bonus if a piece or the king attacks an enemy passer and the square in front of it.
May be I forgot something or not everything is right or important. It is your evaluation that you can improve every time.