When CQ starts up it checks /crx-quickstart/repository/install till CQ5.4
and /crx-quickstart/install CQ5.5 and above use folder for any new package and install them in alphabetical order.
So for example you have a package which has many dependencies, You can rename them in alphabetical order and put them in /crx-quickstart/repository/install folder. Next CQ restart will make sure that they are installed in that order.
For example, If you have Zip file name p001-hotfix-<Some-number>.zip and p002-hotfix-<some-number> under install folder, then p001 will get installed first and then p002 upon restart. After initial installation CQ creates properties file (some thing like <your-package-name>.properties) associated with each package, It is used by installer as a indicator not to install that package again on next restart.
You can also mention start order of package by creating start level folder. For example to assign startlevel 21 to bundle xyz you place the file into crx-quickstart/install/21. The default start level is assigned if you place it into the folder called 0 or directly into the install folder. This is also true for any bundle you put in /install folder in repository (Which is picked up by jcr installer as soon you put them there). Note that number might have preference over alphabets, so rename your files accordingly.
You have to restart CQ after putting files in install folder.
This approach does not work for CRX Hotfix.
Few more facts about packages that is worth mentioning is,
1) If you activate a package from author instance to publish, They get "INSTALLED" on publish instance. In CQ5.5 you have replicate option on package manager it self
For CQ5.4 you have to go to tools->packages-><Your package location> and then click on activate
This is very useful if you have many publish instance and you want to install package to all of them. This is also useful when you have to move package between environments.
2) In cluster instance you only have to install package in one instance (It can be any one, But master is recommended)
I have seen many clients do not know about these features so thought to mention it. Please feel free to comment if you have any question about it.
Caution: Note that, If you use /crx-quickstart/repository/install to install your Hotfix, You might not be able to uninstall it, As no snapshot of that package is created in that case. So if you are testing multiple Hotfix you might want to use package manager in that case.