How to use MS Project in conjunction with a time-tracker tool

In my new job, the company is using a time-tracking tool in a very strict way.
Allow me to explain...
Let's say the project has two phases: Ph1 and Ph2.
Ph1 starts on day 1 and effort is 5 days.
Ph2 starts after Ph1 and effort is 10 days.
There are 3 resources available, R1, R2 and R3, and after a careful estimate of skills and avilability it has been decided the following:
- Ph1 is assigned to R1 from day 1 to day 5, resulting in a duration for Ph1 of 5 days.
- Ph2 is assigned to...
...R2 from day 6 to day 10
...R3 from day 8 to day 12
resulting in a duration of 7 days.
The above is mapped into the time-tracking tool to allow each resource to track time against Ph1 or Ph2 only in the aplanned timeframe. That is: R3 will be able to track
hous aganst Ph2 only from day 8 and only till day 12. That is to avoid that resources track more time that what was originally allocated: if this is necessary, it must be explained why, a new plan must be calculated and more budget must be allocated. When
the ok is given, the tasks in the time-racking tool will be changed accordingly.
If the above situation is clear, my question is: how would you model this in MS Project?
If the WBS in MSP is simply
1. Project X
1.1 Ph1
1.2. Ph2
when allocating R2 and R3 to Ph2, how can I specify that R2 will work only from day 6 to 10 and R3 from day 8 to 12?
At the moment the only clean solution I found is to go into the task usage view and adjust, for each day, the working hours of each resource assigned to the activity.
A second less clean solution is to have a WBS like follows
1. Project X
1.1 Ph1
1.2. Ph2
1.2.1 Ph2.R2
1.2.2 Ph2.R3
that is split Ph2 into two sub-activities, one for each resource.
Thanks fo any help.

Thanks a lot to both of you for your suggestions.
Unfortunately the time-tracking tool cannot be changed: it is a new SAP based tool deployed worldwide.
The problem is that each project involves different teams from differnt countries for a fixed "budget" (or a fixed number of man-days). Therefore there is a global PM in London that will define in the time tracking tool
a WBS like this
1. Project X
1.1 Analysis
1.1.1 Analyse impact for team in Rome
1.1.2 Analyse impact for team in Amsterdam
1.1.3 Analyse impact fr tam in Bangkok
1.2 Development
1.2.1 Develop A
1.2.2 Develop B
1.2.3 Develop C
1.3 Customer Acceptance Test
1.3.1 Prepare test environment by team in Amsterdam
1.3.1 Test by final user
1.3.2 Support user testing by team in Rome
then he would assign the development tasks to the rsources that are supposed to work on it and for only the estimatd time. The reason is easy: he want to make sure that a resource tracks time only against the task she is supposed t work on and for only the
estimated number of days, to avoid exceeding the budget. If extra effort is required for a resource on a task, before allocating more time on that task, a long battle will start.
This we cannot change.
The problem now is on our side, the teams in Rome/Amsterdam/Bangkok: we must keep our own plan in MSP. Our tam in rome is divided in 4 sub-teams, one for each module of the core product, each team with a team
leader assiging tasks to resources with Asana. Untill las week, for months, there was not PM in Rome leading the four teams and hand and of course there was no global plan for the tasks in Rome.
My first attempt was to try with a Gantt that would stop at phases level, without going down to task level, that are under responsibility of the 4 team leaders. the reason being that we have something like
25 projects, some with dependecies with each other. I simply wanted to avoid having one huge MSP file with all projects down to task level: by experience, in my previous project (an ERP upgrade for Oracle EBS in FAO) this approach did not work very well.
But this is bringing up he problem I described: if I stop at "1.2 development" in the WBS, than when I assign R1 and R3, to mak sure their effort is planned accordingly to what has been setup in the time-raking
tool, I need to edit work in the task usage resource by resource, activity by activity.
The other option is to insert under 1.2 development another level with all tasks from Asana, each task being assigned to one resource:
1.2 Development
1.2.1 Develop A
1.2.1.1 Develop class x (by R1)
1.2.1.2 develop class y (by R3)
1.2.2 Develop C
1.2.2.1 Develop new pricing interface (by R4)
1.2.2.2 Modify all logos (by R7)
A third option would be to have one dtailed plan for each project down to the Asana task and then one higher level plan summarising all projects, down to phases only.

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