I looked in my RMSS for answers to your question.
A1) If you look at T-1.6 pg 58 , you can see that in some areas PC's get more than 3 ranks in specific skills. But you also have Hobby ranks. I could not find the exact quote in the book but I am sure that Hobby Ranks are bound by the characters "profession progression".
A2) Apprenticeship and Training package Skill Ranks; pg 266 of RMSS says that TP skills are "special training" that are outside the normal skill buying process. So you can buy more ranks after that. But you also most note that no TP can give the PC more than 10 ranks in any skills. All skill allocations that go beyond the 10 rank are lost with no discount to the TP cost.
A2A) To me that says the PC buys the TP marks off the DP cost then uses the rest of his DP to buy skills. After he is done he applies the ranks for the TP, losing any ranks over 10. This does allow some planing on the players part but to it is not really a big deal in the grand scope of things.
A2B) It is very important to keep track of the little things in TP's. The biggest of these is time. TP's take time to learn and acquire on the players part. Also remember that these TP's may not fit in the GM's game so he may disallow or change any TP in his game. The most common thing that GM's change or throw out is the specials the the TP give, such as money, items and or contacts.
What I do: On a grid sheet [ie skills on the left side and numbered blank boxes across the top] you write the skill name and fill in all the ranks you have from adolescence with a little a. For Hobby Ranks I place a H in each cell so I can tell the difference between a [adolescence or little a] and H [Hobby]. The when I move on for Apprenticeship I use a A [big a] and for each Training Package I use a TP# [TP for Training Package and the number to determine which TP the ranks came from], and I require the player to keep a numbered list of the TP's each has acquired. For levels after App I just use the levels number to represent the skill entry. So 1 rank in a skill at 3rd level is listed in the cell as a 3.
Example: Lets say I have a TP that gives 4 ranks, adol gives 2 ranks, App 3 ranks and 3 Hobby Ranks. In the skill sheet column each entry gets its own cell and would be listed like this Skill: a,a,H,H,H,A,A,A,TP1,TP1. This is because TP's cannot give ranks after the 10th rank. A smart player or a kind GM might point this out to the player so he could change his PC.
I do it this way so I the GM and the player can see where everything came from. Also as a GM I might take a copy of the sheet to keep in my files in case the PC's sheet is destroyed in some way[Usually Pizza grease, soda or beer spill]. This method has helped me in many games to prevent skill bonus explosion and skill bonus creep. It also allows me to have penalties or bonuses be applied to the PC without them noticing it.
I have also tampered with special skill symbolology such as G or GM for GM skill ranks, B for Book skill ranks, M for magic skill ranks and maybe one or two I do not remember right now.
House Rule 1: As a house rule I say that a PC cannot gain more then 10 ranks for a skill by TP's. This is a different than the rule above as it allows the PC to gain more ranks.
House Rule 2: I tend to find beginning PC in RM [1st level] tough to play so I allow the players to create PC of rank 3 if they are pure arms, 4th for semi and 5th for Pure and Hybrid spell casters. To me this allows a good mix of skills and spells and prevents early TPK.
Hope that was not too much info but if you have any more Q's just post them and I will try and answer them.
MDC