Draft pick valuation:
#18 pick (900) received for #31 (600) and #74 (220) - 49ers give enough draft capital for the #21 pick but get #18 instead.
#34 pick (560) surrendered and they receive #40 (500), #216 (6) , and next years 3rd (200?) - they trade 560 in picks to receive 706 in picks
#55 pick (350) received for #61 (292) and #174 (22.8) - They get a pick worth 350 points and only paid 314.8.
#88 pick (150) received for #94 (124) and #216 (6) - They get a pick worth 150 points and only paid 130.
Looking at this, the 49ers are bargain shoppers. They only make a trade that is in their advantage on the old draft value chart. They get maximum value for their picks, but I don't necessarily feel that they are getting a better player when they trade up. For example, chances are Reid would have still been there at #25, but they took him at #18 since he was highest on their board. They simply saw a good trade opportunity, and then chose the best player available to them at that pick.
They are using lower round picks to improve their positioning in the round, so they use a low first and a third to move higher in the first. They do the same thing to convert low seconds and thirds to higher second and third picks. They are not packaging picks to convert lower round picks into higher round picks. One advantage of this approach is that it protects them from a team leap-frogging them to select the player that they had targeted (i.e. Reid being drafted at pick 30 since other teams knew the 49ers wanted a safety). The disadvantage is that they miss out in opportunities to trade their pick for future year picks. The one time they kept a pick (#34), they had an opportunity to trade it for a good future year pick.
So how is Baalke using their picks? They are using them to ensure they have good position in the higher level picks and to get a player that they like instead of the next best available. I would have personally packaged my lower picks into more high picks, but at least they are getting some value in their lower picks, as opposed to just drafting lots of players that won't make the team.